Citrus Sinensis ID: 026646

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-----
Protein Sequence
MEIASSDNSDWLIDYSIVDDIPIAGNFDWPSQAAPAVNASSAASVTIDCSFGDSDGPKEVEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEcccccccccccccccccccccccccccccEEcccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccc
Coil and Loop (DISEMBL)
meiassdnsdwlidysivddipiagnfdwpsqaapavnassaasvtidcsfgdsdgpkeveagsrkrlrsesccvsgskACREKLRRDRLNERFLElgsmlepgrppktdkatILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAmsapsgflphpssmsAAFAAQSQVagnklvpfigypgvamwqfmppaavdtsqdhvlrppva
Flexible Loop (DISEMBL)
meiassdnsdwlIDYSIVDDIPIAGNFDWPSQAAPAVNASSAASVTIDCSFGDSDGPKeveagsrkrlrsesccvsgskacreklrrDRLNERFLelgsmlepgrppktdKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELkaeknelrdEKQRLKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Low Complexity Region (SEG)
MEIASSDNSDWLIDYSIVDDIPIAGNFDWpsqaapavnassaasvTIDCSFGDSDGPKEVEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPssmsaafaaqsqvaGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Disordered region (IsUnstruct)
*********DWLIDYSIVDDIPIAGNFDWPSQA*************I****************************************************************************************************************************************************QVAGNKLVPFIGYPGVAMWQFMPPA***************
Disordered Region (DISOPRED)
*****SD*SDWLIDYSIVDDIP*******************************************************************LNERFLELGSML*********KATILSDAVQMMEQLRTE******************************************************************************************************RPP**
Disordered Region (DISEMBL)
********SDWLIDYSIVDDIPIAGNFDWPSQA*********ASVTIDCSFGD****************************REKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Disordered Region (DISPRO)
*******NSDWLIDYSIVDDIPIAGNFDWPSQAAPAVNASSAASVTID******************************KACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPP**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEIASSDNSDWLIDYSIVDDIPIAGNFDWPSQAAPAVNASSAASVTIDCSFGDSDGPKEVEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATIxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxMSAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
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	235	2.2.26 [Sep-21-2011]
Q9FH37	234	Transcription factor ILR3	yes	no	0.974	0.978	0.626	6e-74
Q9C682	226	Transcription factor bHLH	no	no	0.944	0.982	0.556	4e-66
Q8L467	283	Transcription factor bHLH	no	no	0.693	0.575	0.563	2e-46
Q9LTC7	320	Transcription factor bHLH	no	no	0.714	0.525	0.525	1e-41
Q9LT23	337	Transcription factor bHLH	no	no	0.582	0.406	0.385	1e-20
Q8W2F2	286	Transcription factor bHLH	no	no	0.553	0.454	0.408	2e-18
Q9SN74	240	Transcription factor bHLH	no	no	0.485	0.475	0.304	2e-07
Q9CAD0	596	Transcription factor EGL1	no	no	0.365	0.144	0.306	5e-05
Q1PF16	295	Transcription factor bHLH	no	no	0.425	0.338	0.306	5e-05
Q9LTS4	466	Putative transcription fa	no	no	0.314	0.158	0.381	0.0002

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

 Score =  277 bits (708), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 176/238 (73%), Gaps = 9/238 (3%)

Query: 3   IASSDNSDWLIDYSIVD--DIPIAG-NFDWPSQAAPAVNASSAASVTIDCSFGDSDGPKE 59
           + S +N++W+ D    D     I G  F WP Q    V+++S+A V  D S G+S+  KE
Sbjct: 1   MVSPENANWICDLIDADYGSFTIQGPGFSWPVQQPIGVSSNSSAGV--DGSAGNSEASKE 58

Query: 60  VEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAV 119
              GS+KR R ES   + SKACREK RRDRLN++F+ELG++LEPG PPKTDKA IL DAV
Sbjct: 59  --PGSKKRGRCESSSATSSKACREKQRRDRLNDKFMELGAILEPGNPPKTDKAAILVDAV 116

Query: 120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS- 178
           +M+ QLR EAQKLK SN +LQ+KIKELK EKNELRDEKQRLK +KEKLEQQ+KAM+AP  
Sbjct: 117 RMVTQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQRLKTEKEKLEQQLKAMNAPQP 176

Query: 179 GFLPHPSSMSAAFA-AQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
            F P P  M  AFA AQ Q  GNK+VP I YPGVAMWQFMPPA+VDTSQDHVLRPPVA
Sbjct: 177 SFFPAPPMMPTAFASAQGQAPGNKMVPIISYPGVAMWQFMPPASVDTSQDHVLRPPVA 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 =  251 bits (640), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 169/237 (71%), Gaps = 15/237 (6%)

Query: 3   IASSDNSDWLIDYSIVDDIPIAGNFDWPSQAAPAVNASSAASVTIDCSFGDSDGPKEVEA 62
           + S +N++WL DY +++      N  +P Q    ++ S+  SV +D    D+D  KE   
Sbjct: 1   MVSPENTNWLSDYPLIEGAFSDQNPTFPWQ----IDGSATVSVEVDGFLCDADVIKE--P 54

Query: 63  GSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMM 122
            SRKR+++ESC  S SKACREK RRDRLN++F EL S+LEPGR PKTDK  I++DA++M+
Sbjct: 55  SSRKRIKTESCTGSNSKACREKQRRDRLNDKFTELSSVLEPGRTPKTDKVAIINDAIRMV 114

Query: 123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSG--- 179
            Q R EAQKLK  N +LQEKIKELK EKNELRDEKQ+LK +KE+++QQ+KA+        
Sbjct: 115 NQARDEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQPQPQP 174

Query: 180 -FLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
            FLP+P ++S     Q+Q  G+KLVPF  YPG AMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 175 CFLPNPQTLS-----QAQAPGSKLVPFTTYPGFAMWQFMPPAAVDTSQDHVLRPPVA 226

Arabidopsis thaliana (taxid: 3702)

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

 Score =  185 bits (470), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 98/174 (56%), Positives = 127/174 (72%), Gaps = 11/174 (6%)

Query: 64  SRKRLRSESCCVSG-SKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMM 122
           SRKR R+ SC   G +KACRE+LRR++LNERF++L S+LEPGR PKTDK  IL DA++++
Sbjct: 119 SRKRARTGSCSRGGGTKACRERLRREKLNERFMDLSSVLEPGRTPKTDKPAILDDAIRIL 178

Query: 123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAP-SGFL 181
            QLR EA KL+++N+ L E+IK LKAEKNELR+EK  LKADKEK EQQ+K+M+AP SGF+
Sbjct: 179 NQLRDEALKLEETNQKLLEEIKSLKAEKNELREEKLVLKADKEKTEQQLKSMTAPSSGFI 238

Query: 182 PHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
           PH   + AAF        NK+  +  Y  + MW +MP +  DTS+D  LRPP A
Sbjct: 239 PH---IPAAFNH------NKMAVYPSYGYMPMWHYMPQSVRDTSRDQELRPPAA 283

Arabidopsis thaliana (taxid: 3702)

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

 Score =  169 bits (429), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 94/179 (52%), Positives = 126/179 (70%), Gaps = 11/179 (6%)

Query: 61  EAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQ 120
           E  S KR R+ SC   G+KACREKLRR++LN++F++L S+LEPGR PKTDK+ IL DA++
Sbjct: 149 EECSGKRRRTGSCSKPGTKACREKLRREKLNDKFMDLSSVLEPGRTPKTDKSAILDDAIR 208

Query: 121 MMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS-G 179
           ++ QLR EA +L+++N+ L E+IK LKA+KNELR+EK  LKA+KEK+EQQ+K+M  PS G
Sbjct: 209 VVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLVLKAEKEKMEQQLKSMVVPSPG 268

Query: 180 FLP--HPSSMSAAFAAQSQVAGNKLVPFIGY-PGVAMWQFMPPAAVDTSQDHVLRPPVA 235
           F+P  HP    AAF +          P+  Y P + MW  +PPA  DTS+D    PPVA
Sbjct: 269 FMPSQHP----AAFHSHKMAVA---YPYGYYPPNMPMWSPLPPADRDTSRDLKNLPPVA 320

Arabidopsis thaliana (taxid: 3702)

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

 Score =  100 bits (248), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 67/174 (38%), Positives = 94/174 (54%), Gaps = 37/174 (21%)

Query: 79  KACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNEN 138
           KA REKLRR++LNE F+ELG++L+P RP K DKATIL+D VQ++++L +E  KLK     
Sbjct: 63  KAGREKLRREKLNEHFVELGNVLDPERP-KNDKATILTDTVQLLKELTSEVNKLKSEYTA 121

Query: 139 LQEKIKELKAEKNELRDEKQRLKADKEKL----EQQVKAMS------------------- 175
           L ++ +EL  EKN+LR+EK  LK+D E L    +Q++++MS                   
Sbjct: 122 LTDESRELTQEKNDLREEKTSLKSDIENLNLQYQQRLRSMSPWGAAMDHTVMMAPPPSFP 181

Query: 176 ------APSGFLP-HPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAV 222
                  P G +P HPS  S  +       GN+    I  P      +MPP  V
Sbjct: 182 YPMPIAMPPGSIPMHPSMPSYTY------FGNQNPSMIPAPCPTYMPYMPPNTV 229

Arabidopsis thaliana (taxid: 3702)

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

 Score = 92.8 bits (229), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 58/142 (40%), Positives = 90/142 (63%), Gaps = 12/142 (8%)

Query: 68  LRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRT 127
           ++ E+ C    KA REKLRRD+L E+FLELG+ L+P RP K+DKA++L+D +QM++ +  
Sbjct: 40  VKKEAVC--SQKAEREKLRRDKLKEQFLELGNALDPNRP-KSDKASVLTDTIQMLKDVMN 96

Query: 128 EAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKL----EQQVKAMSAPSGFLPH 183
           +  +LK   E L ++ +EL  EK+ELR+EK  LK+D E L    + ++K M  P  ++PH
Sbjct: 97  QVDRLKAEYETLSQESRELIQEKSELREEKATLKSDIEILNAQYQHRIKTM-VP--WVPH 153

Query: 184 PSSMSAAFAAQSQVAGNKLVPF 205
             S    F A +Q   +  +P+
Sbjct: 154 -YSYHIPFVAITQ-GQSSFIPY 173

Arabidopsis thaliana (taxid: 3702)

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

 Score = 56.2 bits (134), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/115 (30%), Positives = 66/115 (57%), Gaps = 1/115 (0%)

Query: 59  EVEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDA 118
           E  A + +R R        +KA RE+L+R+ LNE F+EL   LE  +   + KA+IL +A
Sbjct: 12  EANATADERCRKGKVPKRINKAVRERLKREHLNELFIELADTLELNQQ-NSGKASILCEA 70

Query: 119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 173
            + ++ +  + + L++ + +L  +   +  EKNEL++E   L+ +  KL+ +++A
Sbjct: 71  TRFLKDVFGQIESLRKEHASLLSESSYVTTEKNELKEETSVLETEISKLQNEIEA 125

Arabidopsis thaliana (taxid: 3702)

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

 Score = 48.1 bits (113), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/88 (30%), Positives = 51/88 (57%), Gaps = 2/88 (2%)

Query: 76  SGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQS 135
           +G+ A  EK RR++LNERF+ L S++      K DK +IL D ++ ++ L+   Q+L+  
Sbjct: 403 TGNHALSEKKRREKLNERFMTLRSIIPS--ISKIDKVSILDDTIEYLQDLQKRVQELESC 460

Query: 136 NENLQEKIKELKAEKNELRDEKQRLKAD 163
            E+   + +    ++ +  DE++R  A+
Sbjct: 461 RESADTETRITMMKRKKPDDEEERASAN 488

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|Q1PF16|BH019_ARATH Transcription factor bHLH19 OS=Arabidopsis thaliana GN=BHLH19 PE=2 SV=1

 Score = 48.1 bits (113), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 58/111 (52%), Gaps = 11/111 (9%)

Query: 27  FDWPSQAAPAVNASSAASVTIDCSFGDSDGPKEVEAGSRKRLRSESCCVSGSKACREKLR 86
           FD+ S     +++ +A  + +D   G     K    G+R      S  ++      E+ R
Sbjct: 77  FDFSSNV---ISSPAAEEIIMDKLVGRGTKRKTCSHGTR------SPVLAKEHVLAERKR 127

Query: 87  RDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNE 137
           R++L+E+F+ L ++L PG   K DK TIL DA+  M+QL+ + + LK+  E
Sbjct: 128 REKLSEKFIALSALL-PGLK-KADKVTILDDAISRMKQLQEQLRTLKEEKE 176

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LTS4|BH041_ARATH Putative transcription factor bHLH041 OS=Arabidopsis thaliana GN=BHLH41 PE=4 SV=1

 Score = 46.2 bits (108), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 47/76 (61%), Gaps = 2/76 (2%)

Query: 83  EKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEK 142
           E+ RR++LNE F  L S+L PG   K DKA++LS A + +  L+ E  KL + N  ++ K
Sbjct: 294 ERKRREKLNESFQALRSLLPPG--TKKDKASVLSIAREQLSSLQGEISKLLERNREVEAK 351

Query: 143 IKELKAEKNELRDEKQ 158
           +   +  +N+LR E++
Sbjct: 352 LAGEREIENDLRPEER 367

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	235
359485584	240	PREDICTED: transcription factor ILR3-lik	0.978	0.958	0.722	1e-95
297739325	223	unnamed protein product [Vitis vinifera]	0.872	0.919	0.785	4e-89
357474831	237	Transcription factor ILR3 [Medicago trun	0.974	0.966	0.676	9e-88
302398597	229	BHLH domain class transcription factor [	0.970	0.995	0.700	6e-85
357474833	261	Transcription factor ILR3 [Medicago trun	0.974	0.877	0.611	5e-83
388521527	238	unknown [Lotus japonicus]	0.978	0.966	0.639	3e-82
359497014	232	PREDICTED: transcription factor ILR3-lik	0.970	0.982	0.644	3e-81
356517276	236	PREDICTED: transcription factor ILR3-lik	0.970	0.966	0.680	6e-81
357452673	230	Transcription factor ILR3 [Medicago trun	0.961	0.982	0.654	1e-80
255563653	235	DNA binding protein, putative [Ricinus c	0.965	0.965	0.676	3e-80

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

 Score =  355 bits (910), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 177/245 (72%), Positives = 203/245 (82%), Gaps = 15/245 (6%)

Query: 1   MEIASSDNSDWLIDYSIVDDIPIAGN----------FDWPSQAAPAVNASSAASVTIDCS 50
           M + SS+NS+WL DY +++DI + G           F WPSQA   + +SS+ S+  DCS
Sbjct: 1   MALDSSENSNWLFDYGLMEDITVPGGEFPEPTPGTGFSWPSQA---LKSSSSVSLEADCS 57

Query: 51  FGDSDGPKEVEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTD 110
           FGDSDG KE+  G RKRL+ ESC  +G+KACREKLRRDRLNERFLELGS+LEPGRPPKTD
Sbjct: 58  FGDSDGLKEL--GPRKRLKHESCGATGTKACREKLRRDRLNERFLELGSILEPGRPPKTD 115

Query: 111 KATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ 170
           KA ILSDAV+M+ QLR+EAQKLK+SN +LQEKIKELKAEKNELRDEKQRLKA+KEKLEQQ
Sbjct: 116 KAAILSDAVRMVTQLRSEAQKLKESNGDLQEKIKELKAEKNELRDEKQRLKAEKEKLEQQ 175

Query: 171 VKAMSAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVL 230
           VKA+SA  GFLPHPS+M AAFAAQ +  GNKL+PFIGYP VAMWQFMPPAAVDTSQDHVL
Sbjct: 176 VKAISAQPGFLPHPSAMPAAFAAQGRAPGNKLMPFIGYPSVAMWQFMPPAAVDTSQDHVL 235

Query: 231 RPPVA 235
           RPPVA
Sbjct: 236 RPPVA 240

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297739325|emb|CBI28976.3| unnamed protein product [Vitis vinifera]

 Score =  333 bits (853), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 165/210 (78%), Positives = 184/210 (87%), Gaps = 5/210 (2%)

Query: 26  NFDWPSQAAPAVNASSAASVTIDCSFGDSDGPKEVEAGSRKRLRSESCCVSGSKACREKL 85
            F WPSQA   + +SS+ S+  DCSFGDSDG KE+  G RKRL+ ESC  +G+KACREKL
Sbjct: 19  GFSWPSQA---LKSSSSVSLEADCSFGDSDGLKEL--GPRKRLKHESCGATGTKACREKL 73

Query: 86  RRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKE 145
           RRDRLNERFLELGS+LEPGRPPKTDKA ILSDAV+M+ QLR+EAQKLK+SN +LQEKIKE
Sbjct: 74  RRDRLNERFLELGSILEPGRPPKTDKAAILSDAVRMVTQLRSEAQKLKESNGDLQEKIKE 133

Query: 146 LKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVAGNKLVPF 205
           LKAEKNELRDEKQRLKA+KEKLEQQVKA+SA  GFLPHPS+M AAFAAQ +  GNKL+PF
Sbjct: 134 LKAEKNELRDEKQRLKAEKEKLEQQVKAISAQPGFLPHPSAMPAAFAAQGRAPGNKLMPF 193

Query: 206 IGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
           IGYP VAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 194 IGYPSVAMWQFMPPAAVDTSQDHVLRPPVA 223

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  328 bits (842), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 163/241 (67%), Positives = 190/241 (78%), Gaps = 12/241 (4%)

Query: 3   IASSDNSDWLIDYSIVDDIPI--------AGNFDWPSQAAPAVNASSAASVTIDCSFGDS 54
           + S +N++W+ DY   DDIP+        +  F WP+Q  P  N SS  S  +D S GDS
Sbjct: 1   MVSRENTNWINDYGFYDDIPVPDSTFALPSSAFTWPTQ--PPFNLSSNVSAEVDGSLGDS 58

Query: 55  DGPKEVEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATI 114
           DG KE  +GS+KR+RSESC  + SKACREKLRRDRLN++F+ELGS+LEPGRP KTDKA I
Sbjct: 59  DGLKE--SGSKKRVRSESCAATSSKACREKLRRDRLNDKFIELGSILEPGRPAKTDKAAI 116

Query: 115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 174
           L DAV+M+ QLR EAQKLK +N  LQEKIKELK EKNELRDEKQRLKA+KEKLEQQ+K+M
Sbjct: 117 LIDAVRMVTQLRGEAQKLKDANSGLQEKIKELKVEKNELRDEKQRLKAEKEKLEQQLKSM 176

Query: 175 SAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPV 234
           +AP  FLP P+++ AAFAAQ Q  GNKLVPFI YPGVAMWQFMPPAAVDTSQDHVLRPPV
Sbjct: 177 NAPPSFLPTPTALPAAFAAQGQAHGNKLVPFISYPGVAMWQFMPPAAVDTSQDHVLRPPV 236

Query: 235 A 235
           A
Sbjct: 237 A 237

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302398597|gb|ADL36593.1| BHLH domain class transcription factor [Malus x domestica]

 Score =  319 bits (818), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 164/234 (70%), Positives = 196/234 (83%), Gaps = 6/234 (2%)

Query: 3   IASSDNSDWLIDYSIVDDIPIA-GNFDWPSQAAPAVNASSAASVTIDCSFGDSDGPKEVE 61
           +AS +N++WL DY ++DD P+  GNF WP Q    +  SS+ASV +D S GD++G KE  
Sbjct: 1   MASPENTNWLFDYGLIDDTPVLDGNFAWPVQP---IAGSSSASVELDGSLGDAEGLKE-- 55

Query: 62  AGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQM 121
           +GS+KR+R+ESC  + SKACREKLRRDRLN++F+ELGS+LEPGRPPKTDKA IL DAV+M
Sbjct: 56  SGSKKRVRTESCSGTSSKACREKLRRDRLNDKFVELGSILEPGRPPKTDKAAILVDAVRM 115

Query: 122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFL 181
           + QLR EAQKLK +N  LQEKIKELKAEKNELRDEKQRLK++KEKLEQQ+K+M+   GFL
Sbjct: 116 VNQLRGEAQKLKDTNSGLQEKIKELKAEKNELRDEKQRLKSEKEKLEQQLKSMNVQPGFL 175

Query: 182 PHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
           P P ++ AAFAAQSQ  GNK+VPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 176 PPPPAIPAAFAAQSQARGNKMVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 229

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  313 bits (801), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 162/265 (61%), Positives = 189/265 (71%), Gaps = 36/265 (13%)

Query: 3   IASSDNSDWLIDYSIVDDIPI--------AGNFDWPSQAAPAVNASSAASVTIDCS---- 50
           + S +N++W+ DY   DDIP+        +  F WP+Q  P  N SS     + CS    
Sbjct: 1   MVSRENTNWINDYGFYDDIPVPDSTFALPSSAFTWPTQ--PPFNLSSNVRSGVRCSNFKQ 58

Query: 51  --------------------FGDSDGPKEVEAGSRKRLRSESCCVSGSKACREKLRRDRL 90
                                GDSDG KE  +GS+KR+RSESC  + SKACREKLRRDRL
Sbjct: 59  CNFPWTDAVDMRMGAEVDGSLGDSDGLKE--SGSKKRVRSESCAATSSKACREKLRRDRL 116

Query: 91  NERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEK 150
           N++F+ELGS+LEPGRP KTDKA IL DAV+M+ QLR EAQKLK +N  LQEKIKELK EK
Sbjct: 117 NDKFIELGSILEPGRPAKTDKAAILIDAVRMVTQLRGEAQKLKDANSGLQEKIKELKVEK 176

Query: 151 NELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPG 210
           NELRDEKQRLKA+KEKLEQQ+K+M+AP  FLP P+++ AAFAAQ Q  GNKLVPFI YPG
Sbjct: 177 NELRDEKQRLKAEKEKLEQQLKSMNAPPSFLPTPTALPAAFAAQGQAHGNKLVPFISYPG 236

Query: 211 VAMWQFMPPAAVDTSQDHVLRPPVA 235
           VAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 237 VAMWQFMPPAAVDTSQDHVLRPPVA 261

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  310 bits (794), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 154/241 (63%), Positives = 185/241 (76%), Gaps = 11/241 (4%)

Query: 3   IASSDNSDWLIDYSIVDDIPIA--------GNFDWPSQAAPAVNASSAASVTIDCSFGDS 54
           + S +N++WL DY ++DDIP            F WPS + P  ++S+   V ID S GDS
Sbjct: 1   MVSRENTNWLFDYGLIDDIPAPEVTFTVPPSGFTWPS-SQPLNSSSNVVGVEIDGSLGDS 59

Query: 55  DGPKEVEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATI 114
           D  KE   GS+KR+RSESC  + SKACREKLRRD+LN++F+ELGS+LEPGRPPKTDKA I
Sbjct: 60  DSLKE--PGSKKRVRSESCSATSSKACREKLRRDKLNDKFVELGSILEPGRPPKTDKAAI 117

Query: 115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 174
           L DAV+M+ QLR EAQK+K +N  LQEKIKELK EKNELRDEKQRLK +KE+LEQQ+K+M
Sbjct: 118 LIDAVRMVTQLRGEAQKMKDTNMGLQEKIKELKTEKNELRDEKQRLKTEKERLEQQLKSM 177

Query: 175 SAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPV 234
           +A   F+P P ++ AAFAAQ Q  GNKLVPFI YPGVAMWQF+PPAA DTSQDH LRPPV
Sbjct: 178 NAQPSFMPPPQALPAAFAAQGQAHGNKLVPFISYPGVAMWQFLPPAARDTSQDHELRPPV 237

Query: 235 A 235
           A
Sbjct: 238 A 238

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359497014|ref|XP_002273184.2| PREDICTED: transcription factor ILR3-like [Vitis vinifera]

 Score =  307 bits (786), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 152/236 (64%), Positives = 185/236 (78%), Gaps = 8/236 (3%)

Query: 3   IASSDNSDWLIDYSIVDDIPIA---GNFDWPSQAAPAVNASSAASVTIDCSFGDSDGPKE 59
           ++  ++ +W+ DY ++DD+P+      F+WPS       AS+A  V  D S  + D  KE
Sbjct: 2   VSPEEDPNWIFDYGLIDDVPVPSLQATFNWPSHD---FTASAALGVEFDDSPVNLDDVKE 58

Query: 60  VEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAV 119
               SRKR+RS  C  SGSKACREK+RRDRLN+RFLELGS+LEPGRPPK DKA ILSDA+
Sbjct: 59  NH--SRKRMRSGLCSASGSKACREKVRRDRLNDRFLELGSILEPGRPPKMDKAVILSDAL 116

Query: 120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSG 179
           +MM QLR+E QKLK+S E+LQEKI ELKAEKNELRDEKQRLK +KE + QQ+KA+S+ +G
Sbjct: 117 RMMTQLRSEGQKLKKSCEDLQEKINELKAEKNELRDEKQRLKTEKENIVQQIKALSSQAG 176

Query: 180 FLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
           FLPHPS++ A FAA  QV G+KL+PFIGYPGV+MWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 177 FLPHPSAIPAPFAAPGQVVGSKLMPFIGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 232

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  306 bits (783), Expect = 6e-81,   Method: Compositional matrix adjust.
 Identities = 164/241 (68%), Positives = 193/241 (80%), Gaps = 13/241 (5%)

Query: 3   IASSDNSDWLIDYSIVDDIPI--------AGNFDWPSQAAPAVNASSAASVTIDCSFGDS 54
           + S +N++WL DY ++DDIP+        +  F WP  A   +NASS   V ID S GDS
Sbjct: 1   MVSRENTNWLFDYGLIDDIPVPDATFGVNSSAFTWPPNA---LNASSNVGVEIDGSLGDS 57

Query: 55  DGPKEVEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATI 114
           D  KE  +GS+KR+RSESC  SGSKACREKLRRDRLN++F+ELG++LEPGRP KTDKA I
Sbjct: 58  DSLKE--SGSKKRVRSESCAASGSKACREKLRRDRLNDKFVELGAILEPGRPAKTDKAAI 115

Query: 115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 174
           L DAV+M+ QLR EAQKLK +N+ LQEKIKELKAEKNELRDEKQRLKA+KEKLEQQ+K++
Sbjct: 116 LIDAVRMVTQLRGEAQKLKDTNQGLQEKIKELKAEKNELRDEKQRLKAEKEKLEQQLKSL 175

Query: 175 SAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPV 234
           +A   F+P P++M AAFAAQ Q  GNKLVPFI YPGVAMWQFMPPAAVDTSQDHVLRPPV
Sbjct: 176 NAQPSFMPPPAAMPAAFAAQGQAHGNKLVPFISYPGVAMWQFMPPAAVDTSQDHVLRPPV 235

Query: 235 A 235
           A
Sbjct: 236 A 236

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  305 bits (780), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 155/237 (65%), Positives = 182/237 (76%), Gaps = 11/237 (4%)

Query: 3   IASSDNSDWLIDYSIVDDIPIAGN----FDWPSQAAPAVNASSAASVTIDCSFGDSDGPK 58
           + S +N++WL DY ++D+IP++ +    F WP       + S+      D S  DSDG K
Sbjct: 1   MVSPENTNWLFDYPLIDEIPVSVDGSFAFTWPPP-----HLSNGGIEMDDSSLVDSDGIK 55

Query: 59  EVEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDA 118
           E   GS+KR RS+SC  S SKACREKLRRDRLN++F+ELGS+LEPGRPPKTDKA IL DA
Sbjct: 56  E--PGSKKRGRSDSCAPSSSKACREKLRRDRLNDKFVELGSILEPGRPPKTDKAAILIDA 113

Query: 119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS 178
           V+M+ QLR EAQKLK SN  LQEKIKELK EKNELRDEKQRLKA+KEKLEQQVK+M+   
Sbjct: 114 VRMVTQLRGEAQKLKDSNSGLQEKIKELKVEKNELRDEKQRLKAEKEKLEQQVKSMNTQP 173

Query: 179 GFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
           GFL HP ++ AAFA Q Q   NKL+PF+ YPGVAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 174 GFLTHPPAIPAAFAHQGQAPSNKLMPFMSYPGVAMWQFMPPAAVDTSQDHVLRPPVA 230

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  304 bits (778), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 163/241 (67%), Positives = 190/241 (78%), Gaps = 14/241 (5%)

Query: 3   IASSDNSDWLIDYSIVDDIPI--------AGNFDWPSQAAPAVNASSAASVTIDCSFGDS 54
           + S +N++WLI+Y ++DDIP+           F WP Q    +N SS  SV ID SFG++
Sbjct: 1   MVSPENTNWLIEYGLIDDIPVPDANFSVPVTGFSWPVQT---LNGSSNVSVEIDGSFGNA 57

Query: 55  DGPKEVEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATI 114
           D  K+  + S+KR RS+SC  S SKACREKLRRDRLN++FLELGS+LEPGRPPKTDKA I
Sbjct: 58  DTQKD--STSKKRGRSDSCA-SSSKACREKLRRDRLNDKFLELGSILEPGRPPKTDKAAI 114

Query: 115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 174
           L DAV+M+ QLR EAQKLK SN +LQEKIKELKAEKNELRDEKQRLK +KEKLEQQ+KA+
Sbjct: 115 LIDAVRMVTQLRGEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKVEKEKLEQQLKAV 174

Query: 175 SAPSGFLPHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPV 234
           +A   FLP P ++ A FAAQ Q  GNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPV
Sbjct: 175 NAQPSFLPPPPAIPAPFAAQGQAPGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPV 234

Query: 235 A 235
           A
Sbjct: 235 A 235

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	235
TAIR|locus:2157538	234	ILR3 "AT5G54680" [Arabidopsis	0.974	0.978	0.571	1.8e-62
UNIPROTKB|Q6ZKI8	253	OJ1119_D01.9 "BHLH transcripti	0.936	0.869	0.487	1.9e-51
UNIPROTKB|Q6ZGM4	236	OJ1442_E05.19 "cDNA clone:006-	0.719	0.716	0.569	5.7e-43
TAIR|locus:2129710	283	bHLH104 "AT4G14410" [Arabidops	0.693	0.575	0.545	5.7e-43
TAIR|locus:2086198	320	bHLH34 "AT3G23210" [Arabidopsi	0.719	0.528	0.511	1.1e-39
UNIPROTKB|Q67U21	343	OSJNBa0065F08.2 "Basic helix-l	0.519	0.355	0.456	5.5e-22
TAIR|locus:2092216	337	bHLH121 "AT3G19860" [Arabidops	0.442	0.308	0.486	6.3e-21
TAIR|locus:2135169	286	bHLH11 "AT4G36060" [Arabidopsi	0.480	0.395	0.435	4.4e-20
UNIPROTKB|Q2R1K8	278	Os11g0601700 "Helix-loop-helix	0.523	0.442	0.341	2.3e-12
UNIPROTKB|Q69V10	265	P0506F02.119 "cDNA clone:J0230	0.395	0.350	0.319	3.5e-11

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

 Score = 638 (229.6 bits), Expect = 1.8e-62, P = 1.8e-62
 Identities = 136/238 (57%), Positives = 160/238 (67%)

Query:     3 IASSDNSDWLIDYSIVD--DIPIAG-NFDWXXXXXXXXXXXXXXXXTIDCSFGDSDGPKE 59
             + S +N++W+ D    D     I G  F W                 +D S G+S+  KE
Sbjct:     1 MVSPENANWICDLIDADYGSFTIQGPGFSWPVQQPIGVSSNSSAG--VDGSAGNSEASKE 58

Query:    60 VEAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAV 119
                GS+KR R ES   + SKACREK RRDRLN++F+ELG++LEPG PPKTDKA IL DAV
Sbjct:    59 --PGSKKRGRCESSSATSSKACREKQRRDRLNDKFMELGAILEPGNPPKTDKAAILVDAV 116

Query:   120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS- 178
             +M+ QLR EAQKLK SN +LQ+KIKELK EKNELRDEKQRLK +KEKLEQQ+KAM+AP  
Sbjct:   117 RMVTQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQRLKTEKEKLEQQLKAMNAPQP 176

Query:   179 GFLPHPXXXXXXXXXXXXXX-GNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
              F P P               GNK+VP I YPGVAMWQFMPPA+VDTSQDHVLRPPVA
Sbjct:   177 SFFPAPPMMPTAFASAQGQAPGNKMVPIISYPGVAMWQFMPPASVDTSQDHVLRPPVA 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 = 534 (193.0 bits), Expect = 1.9e-51, P = 1.9e-51
 Identities = 116/238 (48%), Positives = 150/238 (63%)

Query:    10 DWLIDYSIVDDIPIA--GNFDWXXXXXXXXXXXXXXXXTIDCSFGDSDGPKEVEAGSRKR 67
             DW +D  I++D+P A  G F W                    S+ ++      E GS KR
Sbjct:    22 DWFLDCGILEDLPAAACGAFPWDASPSCSNPSVEVS------SYVNTTSYVLKEPGSNKR 75

Query:    68 LRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRT 127
             +RS SC    SKA REK+RRD++N+RFLELG+ LEPG+P K+DKA ILSDA +M+ QLR 
Sbjct:    76 VRSGSCGRPTSKASREKIRRDKMNDRFLELGTTLEPGKPVKSDKAAILSDATRMVIQLRA 135

Query:   128 EAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPXXX 187
             EA++LK +NE+L++KIKELKAEK+ELRDEKQ+LK +KE LEQQVK ++A   ++PHP   
Sbjct:   136 EAKQLKDTNESLEDKIKELKAEKDELRDEKQKLKVEKETLEQQVKILTATPAYMPHPTLM 195

Query:   188 XX---------XXXXXXXXXGNKLV-PFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
                                 G KL+ PF+GYPG  MWQFMPP+ VDTS+D    PPVA
Sbjct:   196 PAPYPQAPLAPFHHAQGQAAGQKLMMPFVGYPGYPMWQFMPPSEVDTSKDSEACPPVA 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 = 454 (164.9 bits), Expect = 5.7e-43, P = 5.7e-43
 Identities = 103/181 (56%), Positives = 125/181 (69%)

Query:    66 KRLRSESCCVSG--SKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMME 123
             KR R ES   SG  SKACREK+RRDRLN+RFLEL S++ P +  K DKA ILSDA +++ 
Sbjct:    57 KRGRDESSS-SGPKSKACREKIRRDRLNDRFLELSSVINPDKQAKLDKANILSDAARLLA 115

Query:   124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS-APSGF-- 180
             +LR EA+KLK+SNE L+E IK+LK EKNELRDEK  LKA+KE+LEQQVKA+S AP+GF  
Sbjct:   116 ELRGEAEKLKESNEKLRETIKDLKVEKNELRDEKVTLKAEKERLEQQVKALSVAPTGFVP 175

Query:   181 -LPHPXXXXXXXXXXXX----XXGNKLVPF-IGYPGVAMWQFMPPAAVDTSQDHVLRPPV 234
              LPHP                  GNK  P    + G+AMWQ++PP AVDT+QD  L PP 
Sbjct:   176 HLPHPAAFHPAAFPPFIPPYQALGNKNAPTPAAFQGMAMWQWLPPTAVDTTQDPKLWPPN 235

Query:   235 A 235
             A
Sbjct:   236 A 236

GO:0005634 "nucleus" evidence=IC

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

 Score = 454 (164.9 bits), Expect = 5.7e-43, P = 5.7e-43
 Identities = 95/174 (54%), Positives = 123/174 (70%)

Query:    64 SRKRLRSESCCVSG-SKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMM 122
             SRKR R+ SC   G +KACRE+LRR++LNERF++L S+LEPGR PKTDK  IL DA++++
Sbjct:   119 SRKRARTGSCSRGGGTKACRERLRREKLNERFMDLSSVLEPGRTPKTDKPAILDDAIRIL 178

Query:   123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS-GFL 181
              QLR EA KL+++N+ L E+IK LKAEKNELR+EK  LKADKEK EQQ+K+M+APS GF+
Sbjct:   179 NQLRDEALKLEETNQKLLEEIKSLKAEKNELREEKLVLKADKEKTEQQLKSMTAPSSGFI 238

Query:   182 PHPXXXXXXXXXXXXXXGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
             PH                NK+  +  Y  + MW +MP +  DTS+D  LRPP A
Sbjct:   239 PH---------IPAAFNHNKMAVYPSYGYMPMWHYMPQSVRDTSRDQELRPPAA 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 = 423 (154.0 bits), Expect = 1.1e-39, P = 1.1e-39
 Identities = 91/178 (51%), Positives = 121/178 (67%)

Query:    61 EAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQ 120
             E  S KR R+ SC   G+KACREKLRR++LN++F++L S+LEPGR PKTDK+ IL DA++
Sbjct:   149 EECSGKRRRTGSCSKPGTKACREKLRREKLNDKFMDLSSVLEPGRTPKTDKSAILDDAIR 208

Query:   121 MMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS-G 179
             ++ QLR EA +L+++N+ L E+IK LKA+KNELR+EK  LKA+KEK+EQQ+K+M  PS G
Sbjct:   209 VVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLVLKAEKEKMEQQLKSMVVPSPG 268

Query:   180 FLP--HPXXXXXXXXXXXXXXGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235
             F+P  HP              G    P    P + MW  +PPA  DTS+D    PPVA
Sbjct:   269 FMPSQHPAAFHSHKMAVAYPYG--YYP----PNMPMWSPLPPADRDTSRDLKNLPPVA 320

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

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

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

 Score = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 57/125 (45%), Positives = 78/125 (62%)

Query:    48 DCSFGDSDGPKEVEAGSRKRLRSESCCVSGS--KACREKLRRDRLNERFLELGSMLEPGR 105
             D  F   DG    ++  +   +++    +    KA REK+RRDRLNE+F ELGS L+P R
Sbjct:    11 DGFFHPRDGACPADSSGKTECKTQGSIATRKVQKADREKMRRDRLNEQFQELGSTLDPDR 70

Query:   106 PPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKE 165
             P + DKATILSDA+QM++ L ++  KLK    +L E+ +EL  EKNELRDEK  LK + +
Sbjct:    71 P-RNDKATILSDAIQMLKDLTSQVNKLKAEYTSLSEEARELTQEKNELRDEKVSLKFEVD 129

Query:   166 KLEQQ 170
              L  Q
Sbjct:   130 NLNTQ 134

GO:0005634 "nucleus" evidence=IC

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

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 53/109 (48%), Positives = 77/109 (70%)

Query:    79 KACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNEN 138
             KA REKLRR++LNE F+ELG++L+P RP K DKATIL+D VQ++++L +E  KLK     
Sbjct:    63 KAGREKLRREKLNEHFVELGNVLDPERP-KNDKATILTDTVQLLKELTSEVNKLKSEYTA 121

Query:   139 LQEKIKELKAEKNELRDEKQRLKADKEKL----EQQVKAMSAPSGFLPH 183
             L ++ +EL  EKN+LR+EK  LK+D E L    +Q++++MS     + H
Sbjct:   122 LTDESRELTQEKNDLREEKTSLKSDIENLNLQYQQRLRSMSPWGAAMDH 170

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

 Score = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 51/117 (43%), Positives = 78/117 (66%)

Query:    68 LRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRT 127
             ++ E+ C    KA REKLRRD+L E+FLELG+ L+P RP K+DKA++L+D +QM++ +  
Sbjct:    40 VKKEAVC--SQKAEREKLRRDKLKEQFLELGNALDPNRP-KSDKASVLTDTIQMLKDVMN 96

Query:   128 EAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK-AMSAPSGFLPH 183
             +  +LK   E L ++ +EL  EK+ELR+EK  LK+D E L  Q +  +     ++PH
Sbjct:    97 QVDRLKAEYETLSQESRELIQEKSELREEKATLKSDIEILNAQYQHRIKTMVPWVPH 153

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

 Score = 167 (63.8 bits), Expect = 2.3e-12, P = 2.3e-12
 Identities = 43/126 (34%), Positives = 70/126 (55%)

Query:    50 SFGDSDGPKEVEA--GSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPP 107
             S G S      +A  GS  +   E       KA REKL+RD+LN+ F+EL SML+P R  
Sbjct:    20 SLGGSSNAASDKAVDGSLDKRSQEKAPKKTHKAEREKLKRDQLNDLFVELSSMLDPERQ- 78

Query:   108 KTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKL 167
              + KAT+L DA +++  L ++ + L++    L  + + + +E NEL++E   L+A   +L
Sbjct:    79 NSGKATVLGDAARVLRDLVSQVESLRKEQSALLTERQYVGSENNELQEENIMLRAQILEL 138

Query:   168 EQQVKA 173
               ++ A
Sbjct:   139 HNEICA 144

GO:0005634 "nucleus" evidence=IC

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

 Score = 156 (60.0 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 30/94 (31%), Positives = 60/94 (63%)

Query:    79 KACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNEN 138
             K+ REKL+RD+ N+ F ELG++LEP R     KA +L +  ++++ L ++ + L++ N +
Sbjct:    40 KSEREKLKRDKQNDLFNELGNLLEPDRQ-NNGKACVLGETTRILKDLLSQVESLRKENSS 98

Query:   139 LQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 172
             L+ +   +  E+NEL D+   L+ +  +L+ +++
Sbjct:    99 LKNESHYVALERNELHDDNSMLRTEILELQNELR 132

GO:0005634 "nucleus" evidence=IC

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9FH37	ILR3_ARATH	No assigned EC number	0.6260	0.9744	0.9786	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	235
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	1e-08
smart00353	53	smart00353, HLH, helix loop helix domain	1e-08
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	4e-08
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-05
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	2e-05
pfam13870	177	pfam13870, DUF4201, Domain of unknown function (DU	3e-05
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	3e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	9e-05
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	2e-04
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
pfam12329	74	pfam12329, TMF_DNA_bd, TATA element modulatory fac	2e-04
pfam04111	356	pfam04111, APG6, Autophagy protein Apg6	2e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	3e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	3e-04
pfam04977	80	pfam04977, DivIC, Septum formation initiator	5e-04
TIGR02894	161	TIGR02894, DNA_bind_RsfA, transcription factor, Rs	5e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	6e-04
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	6e-04
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	7e-04
PRK13729	475	PRK13729, PRK13729, conjugal transfer pilus assemb	7e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-04
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	8e-04
TIGR00019	360	TIGR00019, prfA, peptide chain release factor 1	8e-04
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	9e-04
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	0.001
COG4026	290	COG4026, COG4026, Uncharacterized protein containi	0.001
smart00338	65	smart00338, BRLZ, basic region leucin zipper	0.001
pfam07926	132	pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein	0.001
pfam06005	72	pfam06005, DUF904, Protein of unknown function (DU	0.001
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	0.002
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.002
TIGR02894	161	TIGR02894, DNA_bind_RsfA, transcription factor, Rs	0.002
pfam06005	72	pfam06005, DUF904, Protein of unknown function (DU	0.002
pfam10211	189	pfam10211, Ax_dynein_light, Axonemal dynein light	0.002
pfam01025	165	pfam01025, GrpE, GrpE	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.003
PRK05771	646	PRK05771, PRK05771, V-type ATP synthase subunit I;	0.003
cd12193	54	cd12193, B_zip1, basic leucine zipper DNA-binding	0.003
pfam09798	648	pfam09798, LCD1, DNA damage checkpoint protein	0.003
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.004

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

 Score = 49.8 bits (120), Expect = 1e-08
 Identities = 18/49 (36%), Positives = 28/49 (57%)

Query: 78  SKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLR 126
           +   RE+ RRDR+N+ F EL  +L      K  KA IL  A++ ++ L+
Sbjct: 4   AHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

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

 Score = 49.5 bits (119), Expect = 1e-08
 Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 82  REKLRRDRLNERFLELGSMLEPGRPP-KTDKATILSDAVQMMEQLRTEAQK 131
           RE+ RR ++NE F EL S+L       K  KA IL  A++ ++ L+ E QK
Sbjct: 3   RERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

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

 Score = 48.4 bits (116), Expect = 4e-08
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 78  SKACREKLRRDRLNERFLELGSML-EPGRPPKTDKATILSDAVQMMEQLRTEAQ 130
           +   RE+ RR+R+N+ F EL S+L       K  KA IL  AV  ++ L+   Q
Sbjct: 7   AHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 45.5 bits (108), Expect = 1e-05
 Identities = 21/96 (21%), Positives = 45/96 (46%), Gaps = 5/96 (5%)

Query: 79   KACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNEN 138
            +    + + +RL     EL   LE          T+ ++  + +E+L  E + L   N  
Sbjct: 913  RLEELEAKLERLEVELPELEEELEEEYE-----DTLETELEREIERLEEEIEALGPVNLR 967

Query: 139  LQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 174
              E+ +E++    EL+ +++ L+  KEKL + ++ +
Sbjct: 968  AIEEYEEVEERYEELKSQREDLEEAKEKLLEVIEEL 1003

Length = 1163

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

 Score = 43.5 bits (103), Expect = 2e-05
 Identities = 17/53 (32%), Positives = 34/53 (64%)

Query: 118 AVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ 170
           A + + +L+ E  +L++    LQE++ EL+ E  EL+ E   L+A+ E+L+++
Sbjct: 64  ARERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKE 116

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|222426 pfam13870, DUF4201, Domain of unknown function (DUF4201)

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 18/69 (26%), Positives = 39/69 (56%)

Query: 119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS 178
           V ++  L+ +   L++  E L++++KE +    +LR E  ++K +++KL +Q K +    
Sbjct: 76  VHILTHLKEKLHMLEEELERLKKELKEKEERLAKLRKELYKVKLERDKLRKQNKKLRQQG 135

Query: 179 GFLPHPSSM 187
           G L  P+ +
Sbjct: 136 GLLHVPALL 144

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

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

 Score = 43.7 bits (104), Expect = 3e-05
 Identities = 16/48 (33%), Positives = 30/48 (62%)

Query: 122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ 169
           +E L     +L++    L+ K+++L+AE  +L  E +RLK++ EKL+ 
Sbjct: 3   LEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKS 50

Length = 389

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

 Score = 42.8 bits (101), Expect = 9e-05
 Identities = 28/90 (31%), Positives = 43/90 (47%)

Query: 86  RRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKE 145
           +R  L E   EL   LE            L    Q  E+L  E ++L++  E L+EK+ E
Sbjct: 787 KRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDE 846

Query: 146 LKAEKNELRDEKQRLKADKEKLEQQVKAMS 175
           L+ E  EL  E + LK + E+LE + + + 
Sbjct: 847 LEEELEELEKELEELKEELEELEAEKEELE 876

Length = 1163

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

 Score = 41.1 bits (97), Expect = 2e-04
 Identities = 15/65 (23%), Positives = 39/65 (60%), Gaps = 3/65 (4%)

Query: 115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLK---ADKEKLEQQV 171
           L++  + + +L+ +  +L+Q N+ L++++  L+AE   L+ E  R+K   A+  +L+++ 
Sbjct: 75  LAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEEN 134

Query: 172 KAMSA 176
           + +  
Sbjct: 135 RELRE 139

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 = 2e-04
 Identities = 12/54 (22%), Positives = 34/54 (62%)

Query: 128 EAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFL 181
             + L++ N  L+E+I++L+ +  +L  E ++L+ + E+L+ +++ + +P   +
Sbjct: 2   RLEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSPPLIV 55

Length = 389

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

 Score = 41.7 bits (98), Expect = 2e-04
 Identities = 21/84 (25%), Positives = 41/84 (48%)

Query: 87  RDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKEL 146
            + L ER  EL    E     K     I S  ++ ++    E ++L++  E L+EKI+ L
Sbjct: 234 IEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERL 293

Query: 147 KAEKNELRDEKQRLKADKEKLEQQ 170
           +  + E+ + ++ L+  +  LE+ 
Sbjct: 294 EELEREIEELEEELEGLRALLEEL 317

Length = 908

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 18/52 (34%), Positives = 28/52 (53%)

Query: 120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV 171
           + + QL  E +KL +        IK+L+A+  EL  E   LK   EKLE+++
Sbjct: 12  EQIAQLMEEGEKLSKKELKHNNTIKKLRAKNKELEKEIAELKKKLEKLEKEL 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|217902 pfam04111, APG6, Autophagy protein Apg6

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 17/48 (35%), Positives = 31/48 (64%)

Query: 123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ 170
           E L +E  +LK+  E L ++++EL+ E ++L  E   L+ +KE+LE +
Sbjct: 66  EALDSELDELKKEEERLLDELEELEKEDDDLDGELVELQEEKEQLENE 113

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

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

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 20/90 (22%), Positives = 41/90 (45%)

Query: 83  EKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEK 142
             L     + R  E+ + L       +     L +  Q + +L  E + L++  + LQE+
Sbjct: 782 NDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQ 841

Query: 143 IKELKAEKNELRDEKQRLKADKEKLEQQVK 172
             +LK +   +  E + L   KE+LE++++
Sbjct: 842 RIDLKEQIKSIEKEIENLNGKKEELEEELE 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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.2 bits (97), Expect = 3e-04
 Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 7/96 (7%)

Query: 87  RDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKEL 146
              L +   EL   LE  R    + +  +S   + + +L  E ++L++    L +++ EL
Sbjct: 700 LAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTEL 759

Query: 147 KAEK-------NELRDEKQRLKADKEKLEQQVKAMS 175
           +AE         E  +E    +A+ E+LE Q++ + 
Sbjct: 760 EAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLK 795

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|203138 pfam04977, DivIC, Septum formation initiator

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 15/43 (34%), Positives = 26/43 (60%)

Query: 130 QKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 172
            +L Q    LQ ++ +LKAE  EL  E + LK+D + +E++ +
Sbjct: 20  YQLNQEIAALQAELAKLKAENEELEAEVKDLKSDPDYIEERAR 62

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

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

 Score = 39.0 bits (91), Expect = 5e-04
 Identities = 15/46 (32%), Positives = 28/46 (60%)

Query: 122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKL 167
            + L+ E ++LK  NE+LQ++ +EL+ E  +LR     ++ D + L
Sbjct: 99  DQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTL 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 = 40.4 bits (95), Expect = 6e-04
 Identities = 25/95 (26%), Positives = 49/95 (51%), Gaps = 14/95 (14%)

Query: 82  REKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQE 141
            E+ RRD+L E + EL                 L D    +E++  E  + +   ++ +E
Sbjct: 347 EERKRRDKLTEEYAEL--------------KEELEDLRAELEEVDKEFAETRDELKDYRE 392

Query: 142 KIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA 176
           K+++LK E NEL+ E  RL+ + ++L +++  ++A
Sbjct: 393 KLEKLKREINELKRELDRLQEELQRLSEELADLNA 427

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|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 40.2 bits (95), Expect = 6e-04
 Identities = 15/56 (26%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKA--DKEKLEQQVKA 173
           +++  L    ++L+Q  E  +  +KE +  K EL ++K++L+   DK   E + +A
Sbjct: 520 ELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEA 575

Length = 782

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 40.2 bits (94), Expect = 7e-04
 Identities = 15/49 (30%), Positives = 29/49 (59%)

Query: 120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE 168
            ++E+L    ++L+Q NE+L++ +KE +  K EL  E + LK  +   +
Sbjct: 515 VLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKK 563

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 [DNA metabolism, Other]. Length = 771

>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB; Provisional

 Score = 39.8 bits (93), Expect = 7e-04
 Identities = 27/125 (21%), Positives = 45/125 (36%), Gaps = 16/125 (12%)

Query: 109 TDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE 168
           T+     +   +  E++R E   L +   + Q +I++L  +   L ++   +KA      
Sbjct: 72  TEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQ---VKALGANPV 128

Query: 169 ----QQVKAMSAPSGFL---PHPSSMSAAFAAQSQVAGNKLVPFIGYPGVAMWQFMPPAA 221
               + V  M A        P P +   +F  Q  VA      F  YPG      + P  
Sbjct: 129 TATGEPVPQMPASPPGPEGEPQPGNTPVSFPPQGSVAVPPPTAF--YPGNG----VTPPP 182

Query: 222 VDTSQ 226
             T Q
Sbjct: 183 QVTYQ 187

Length = 475

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

 Score = 40.1 bits (94), Expect = 8e-04
 Identities = 17/68 (25%), Positives = 36/68 (52%)

Query: 109 TDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE 168
              + +L +  ++ E LR E  +L+     ++ +++ELK E   L +  +RL    E L+
Sbjct: 365 EKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLK 424

Query: 169 QQVKAMSA 176
           +++K + A
Sbjct: 425 EELKELEA 432

Length = 1163

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

 Score = 40.1 bits (94), Expect = 8e-04
 Identities = 26/93 (27%), Positives = 52/93 (55%), Gaps = 9/93 (9%)

Query: 83  EKLRRDRLN-ERFLELGSMLEPGRPPKTDKATILSDAVQMMEQL---RTEAQKLKQSNEN 138
           EKL R     ER+ EL + L      + + A +L+   ++ ++L     E  +L++  E 
Sbjct: 203 EKLERQAEKAERYQELKAELR-----ELELALLLAKLKELRKELEELEEELSRLEEELEE 257

Query: 139 LQEKIKELKAEKNELRDEKQRLKADKEKLEQQV 171
           LQE+++E + E  EL+ E + L+ + E+L++++
Sbjct: 258 LQEELEEAEKEIEELKSELEELREELEELQEEL 290

Length = 1163

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

 Score = 38.8 bits (91), Expect = 8e-04
 Identities = 18/63 (28%), Positives = 32/63 (50%)

Query: 114 ILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 173
           +LS  +      R    +L+Q    LQE++ EL+ +  EL+ E Q LK +   LE +++ 
Sbjct: 53  VLSRYLSDTPSARERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELER 112

Query: 174 MSA 176
           +  
Sbjct: 113 LQK 115

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|129130 TIGR00019, prfA, peptide chain release factor 1

 Score = 39.7 bits (93), Expect = 8e-04
 Identities = 25/95 (26%), Positives = 50/95 (52%), Gaps = 5/95 (5%)

Query: 88  DRLNERFLELGSML-EPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKEL 146
           + L ER+ EL ++L +P      DK   LS     +E++    ++ +Q+ E+++E  + L
Sbjct: 10  ESLLERYEELEALLSDPEVISDQDKLRKLSKEYSQLEEIVDCYREYQQAQEDIKEAKEIL 69

Query: 147 KAEKNELRDEKQ----RLKADKEKLEQQVKAMSAP 177
           +    E+R+  +     L+   E+LE+Q+K +  P
Sbjct: 70  EESDPEMREMAKEELEELEEKIEELEEQLKVLLLP 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 = 38.8 bits (91), Expect = 9e-04
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 3/65 (4%)

Query: 115 LSDAVQMMEQLRTEAQKLKQSNENLQ---EKIKELKAEKNELRDEKQRLKADKEKLEQQV 171
           L++  Q  ++L+ E   L+   E LQ    +IK+L A   EL +E + L+ +  +L+Q+ 
Sbjct: 89  LAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEENRELREELAELKQEN 148

Query: 172 KAMSA 176
           +A+ A
Sbjct: 149 EALEA 153

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|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 29/106 (27%), Positives = 46/106 (43%), Gaps = 9/106 (8%)

Query: 75  VSGSKACREKLRR-----DRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEA 129
           +S + + RE+L         L E   EL   L   +    +    LS     +E+L+ E 
Sbjct: 58  LSDTPSARERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKEL 117

Query: 130 QKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS 175
            ++KQ + N      EL  E  ELR+E   LK + E LE + + + 
Sbjct: 118 ARIKQLSAN----AIELDEENRELREELAELKQENEALEAENERLQ 159

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

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

 Score = 39.1 bits (91), Expect = 0.001
 Identities = 16/58 (27%), Positives = 38/58 (65%)

Query: 115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 172
             D  +  E+L+ + ++L++  E L ++++EL+AE  E+++  +RL+ +  +LE+ +K
Sbjct: 130 YMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLK 187

Length = 290

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 14/44 (31%), Positives = 29/44 (65%)

Query: 130 QKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 173
           ++ K   E L+ K+++L+AE   L+ E +RL+ + EKL+ +++ 
Sbjct: 22  ERKKAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSELEE 65

Length = 65

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 12/61 (19%), Positives = 36/61 (59%), Gaps = 4/61 (6%)

Query: 116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRD----EKQRLKADKEKLEQQV 171
           ++ ++ ++ LR +  +LK+    L+ + +  +AE +E  +    +K+ L+ +  +LE+++
Sbjct: 55  AEDIEELQALRKQLNELKKEIAQLKAEAESAQAELSEAEESWEEQKKMLEDELSELEKRI 114

Query: 172 K 172
           +
Sbjct: 115 E 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 = 36.5 bits (85), Expect = 0.001
 Identities = 15/51 (29%), Positives = 35/51 (68%)

Query: 120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ 170
           +++E+L ++ Q+  ++   LQ +I+ELK E  +L +E + L+ + +KL+++
Sbjct: 4   ELLEELESKIQQAVETIALLQMEIEELKEENEQLSEENEELEEENKKLKEE 54

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

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

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 16/52 (30%), Positives = 30/52 (57%)

Query: 115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEK 166
           L   +  ++QL   A +L + N  L+E++ ELK E   L  E +RL+ ++++
Sbjct: 113 LQKELARIKQLSANAIELDEENRELREELAELKQENEALEAENERLQENEQR 164

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

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

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 18/48 (37%), Positives = 29/48 (60%)

Query: 123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ 170
           EQL  E +KLK+  E L+E +  L+ E   ++ E + L+A  E+LE+ 
Sbjct: 726 EQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEED 773

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

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

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 115 LSDAVQMMEQLRT---EAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV 171
           L D +  ++ L+T     Q L++ NE L+ + + L+    EL  E ++L+     +E+  
Sbjct: 82  LQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDY 141

Query: 172 KAM 174
           + +
Sbjct: 142 QTL 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|203371 pfam06005, DUF904, Protein of unknown function (DUF904)

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 4/56 (7%)

Query: 118 AVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDE----KQRLKADKEKLEQ 169
           AV+ +  L+ E ++LK+ NE L E+ +EL+ E  +L++E    + RL+A   KL++
Sbjct: 16  AVETIALLQMEIEELKEENEQLSEENEELEEENKKLKEERNAWQSRLRALLGKLDE 71

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

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

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 15/70 (21%)

Query: 120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNEL--RDEKQR-------------LKADK 164
           Q   +L  E +KL++  E L++++ EL+A+   +  R+E++R             LK   
Sbjct: 120 QGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREEEERQIEEKRHADEIAFLKKQN 179

Query: 165 EKLEQQVKAM 174
           ++L+ Q++ +
Sbjct: 180 QQLKSQLEQI 189

Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains. Length = 189

>gnl|CDD|216249 pfam01025, GrpE, GrpE

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 15/46 (32%), Positives = 28/46 (60%)

Query: 127 TEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 172
            E ++L+   E L+E+++EL+ E  EL+D   RL A+ E   ++ +
Sbjct: 4   EEEEELEDEEEALEEELEELEEEIEELKDRLLRLLAEFENYRKRTE 49

Length = 165

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

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 22/97 (22%), Positives = 48/97 (49%), Gaps = 2/97 (2%)

Query: 82  REKLRR--DRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENL 139
            E+L    +    R   L   LE     +      + +  + +E+L  +  +L++  E L
Sbjct: 795 LEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEEL 854

Query: 140 QEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA 176
           +++++ELK E  EL  EK+ L+ + ++LE++ + +  
Sbjct: 855 EKELEELKEELEELEAEKEELEDELKELEEEKEELEE 891

Length = 1163

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

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 23/88 (26%), Positives = 44/88 (50%)

Query: 82  REKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQE 141
             +   + L E   E    L+                 Q +E+L  E ++L++  + L+E
Sbjct: 790 ALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEE 849

Query: 142 KIKELKAEKNELRDEKQRLKADKEKLEQ 169
           +++EL+ E  EL++E + L+A+KE+LE 
Sbjct: 850 ELEELEKELEELKEELEELEAEKEELED 877

Length = 1163

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

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 22/91 (24%), Positives = 49/91 (53%)

Query: 86  RRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKE 145
           R   L  +  EL + LE       + A  L++  + +E+L+ E + L+   E L+ +++E
Sbjct: 310 RLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEE 369

Query: 146 LKAEKNELRDEKQRLKADKEKLEQQVKAMSA 176
           L++   EL ++ + L++   +LE Q+ +++ 
Sbjct: 370 LESRLEELEEQLETLRSKVAQLELQIASLNN 400

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

 Score = 38.4 bits (90), Expect = 0.003
 Identities = 26/102 (25%), Positives = 46/102 (45%), Gaps = 12/102 (11%)

Query: 71  ESCCVSGSKACREKLRRDR--LNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTE 128
           E      S     KLR     L+E   +L S L         K   L +  + +     E
Sbjct: 34  EDLKEELSNERLRKLRSLLTKLSEALDKLRSYLP--------KLNPLREEKKKVSVKSLE 85

Query: 129 --AQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE 168
              + +++  E ++++IKEL+ E +EL +E + L+ + E+LE
Sbjct: 86  ELIKDVEEELEKIEKEIKELEEEISELENEIKELEQEIERLE 127

Length = 646

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

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 13/40 (32%), Positives = 23/40 (57%)

Query: 123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKA 162
           E  R    +  +  + L++K++EL +E ++L DE  RLK 
Sbjct: 12  EAARRSRARKMERMKQLEDKVEELTSENSDLEDEVDRLKK 51

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

>gnl|CDD|220410 pfam09798, LCD1, DNA damage checkpoint protein

 Score = 37.9 bits (88), Expect = 0.003
 Identities = 25/95 (26%), Positives = 41/95 (43%), Gaps = 7/95 (7%)

Query: 114 ILSDAVQMME-QLRTEAQKLKQSNENLQEK----IKELKAEKNELRDEKQRLKADKEKLE 168
           +L D + M++ Q + E  K K     L+EK    +++LK E   L DE++ L  ++  L 
Sbjct: 1   MLRDKLDMLQQQKQEERNKQKSRVNELKEKHDQELQKLKQELQSLEDERKFLVLEQRGLS 60

Query: 169 --QQVKAMSAPSGFLPHPSSMSAAFAAQSQVAGNK 201
                  +S PS  L    +   A  +Q      K
Sbjct: 61  ANDLRTELSPPSNLLKTSDASHIADESQPNSIKQK 95

This is a family of proteins which regulate checkpoint kinases. In Schizosaccharomyces pombe this protein is called Rad26 and in Saccharomyces cerevisiae it is called LCD1. Length = 648

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

 Score = 37.7 bits (88), Expect = 0.004
 Identities = 19/72 (26%), Positives = 42/72 (58%)

Query: 101 LEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRL 160
           +    P   ++   L   V+ +E+L+ E ++L++  E+L+   ++L+ +  EL +  + L
Sbjct: 212 ISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEEL 271

Query: 161 KADKEKLEQQVK 172
           K + E+LE++VK
Sbjct: 272 KKEIEELEEKVK 283

Length = 880

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	235
KOG1318	411	consensus Helix loop helix transcription factor EB	99.47
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.47
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.45
smart00353	53	HLH helix loop helix domain.	99.43
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	99.16
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.93
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.66
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.55
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.43
KOG0561	373	consensus bHLH transcription factor [Transcription	98.31
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.79
PLN03217	93	transcription factor ATBS1; Provisional	97.61
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.53
PRK15422	79	septal ring assembly protein ZapB; Provisional	97.38
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	97.24
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	97.21
KOG3910	632	consensus Helix loop helix transcription factor [T	97.09
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	96.84
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	96.62
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	96.43
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	95.95
PRK15422	79	septal ring assembly protein ZapB; Provisional	95.75
smart00338	65	BRLZ basic region leucin zipper.	95.62
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	95.51
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	95.37
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	95.21
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	94.97
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	94.77
PRK13169	110	DNA replication intiation control protein YabA; Re	94.72
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	94.69
PRK10884	206	SH3 domain-containing protein; Provisional	94.61
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	94.13
KOG3582	856	consensus Mlx interactors and related transcriptio	94.09
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	94.03
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	94.01
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	93.95
COG4026	290	Uncharacterized protein containing TOPRIM domain,	93.77
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	93.67
PRK11637	428	AmiB activator; Provisional	93.62
PRK13169	110	DNA replication intiation control protein YabA; Re	93.59
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	93.56
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	93.5
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	93.47
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	93.4
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	93.39
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	93.32
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	93.12
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	92.8
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	92.74
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	92.72
KOG3650	120	consensus Predicted coiled-coil protein [General f	92.6
PF13815	118	Dzip-like_N: Iguana/Dzip1-like DAZ-interacting pro	92.6
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	92.56
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	92.39
PRK10884	206	SH3 domain-containing protein; Provisional	92.36
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	92.26
PRK02119	73	hypothetical protein; Provisional	92.1
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	91.95
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	91.94
PRK04406	75	hypothetical protein; Provisional	91.84
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	91.84
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	91.51
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	91.47
PRK11637	428	AmiB activator; Provisional	91.46
KOG0996	1293	consensus Structural maintenance of chromosome pro	91.43
COG4026	290	Uncharacterized protein containing TOPRIM domain,	91.38
PF04880	166	NUDE_C: NUDE protein, C-terminal conserved region;	91.16
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	91.03
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	90.92
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	90.75
PHA02562	562	46 endonuclease subunit; Provisional	90.62
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	90.54
PRK00846	77	hypothetical protein; Provisional	90.46
smart00338	65	BRLZ basic region leucin zipper.	90.37
KOG3119	269	consensus Basic region leucine zipper transcriptio	90.34
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	90.3
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	90.27
TIGR02209	85	ftsL_broad cell division protein FtsL. This model	90.24
COG4467	114	Regulator of replication initiation timing [Replic	90.17
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	90.12
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	90.1
PF12808	52	Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2	90.1
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	90.03
KOG2391	365	consensus Vacuolar sorting protein/ubiquitin recep	90.02
PRK04325	74	hypothetical protein; Provisional	89.96
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	89.89
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	89.82
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	89.8
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	89.71
TIGR02231	525	conserved hypothetical protein. This family consis	89.62
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	89.6
PF04420	161	CHD5: CHD5-like protein; InterPro: IPR007514 Membe	89.55
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	89.3
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	89.25
PRK00295	68	hypothetical protein; Provisional	89.24
KOG1962	216	consensus B-cell receptor-associated protein and r	89.19
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	89.17
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	89.09
KOG3898	254	consensus Transcription factor NeuroD and related	88.99
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	88.95
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	88.9
KOG3119	269	consensus Basic region leucine zipper transcriptio	88.81
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	88.8
PRK02793	72	phi X174 lysis protein; Provisional	88.75
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	88.72
KOG4395	285	consensus Transcription factor Atonal, contains HT	88.62
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	88.54
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	88.51
PF07989	75	Microtub_assoc: Microtubule associated; InterPro:	88.47
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	88.41
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	88.33
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	88.27
PRK13922	276	rod shape-determining protein MreC; Provisional	88.23
PF14662	193	CCDC155: Coiled-coil region of CCDC155	88.2
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	88.12
PF06785	401	UPF0242: Uncharacterised protein family (UPF0242);	87.96
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	87.94
COG4942	420	Membrane-bound metallopeptidase [Cell division and	87.87
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	87.82
PRK09039	343	hypothetical protein; Validated	87.78
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	87.53
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	87.51
PF10186	302	Atg14: UV radiation resistance protein and autopha	87.2
PRK00736	68	hypothetical protein; Provisional	87.07
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	86.91
PHA03011	120	hypothetical protein; Provisional	86.9
PF10498	359	IFT57: Intra-flagellar transport protein 57 ; Inte	86.88
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	86.48
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	86.48
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	86.47
COG2433	652	Uncharacterized conserved protein [Function unknow	86.45
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	86.44
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	86.21
PRK00888	105	ftsB cell division protein FtsB; Reviewed	86.15
PRK00888	105	ftsB cell division protein FtsB; Reviewed	86.11
KOG0946	970	consensus ER-Golgi vesicle-tethering protein p115	86.08
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	86.05
PRK13922	276	rod shape-determining protein MreC; Provisional	85.95
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	85.82
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	85.74
KOG4571	294	consensus Activating transcription factor 4 [Trans	85.73
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	85.65
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	85.45
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	85.41
COG1256	552	FlgK Flagellar hook-associated protein [Cell motil	85.33
PF07889	126	DUF1664: Protein of unknown function (DUF1664); In	85.16
PF01166	59	TSC22: TSC-22/dip/bun family; InterPro: IPR000580	85.1
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	85.0
KOG4797	123	consensus Transcriptional regulator [Transcription	84.98
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	84.91
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	84.9
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	84.81
PF15458	254	NTR2: Nineteen complex-related protein 2	84.58
PF14662	193	CCDC155: Coiled-coil region of CCDC155	84.58
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	84.57
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	84.48
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	84.26
PF00038	312	Filament: Intermediate filament protein; InterPro:	83.98
PF05103	131	DivIVA: DivIVA protein; InterPro: IPR007793 The Ba	83.86
PRK03992	389	proteasome-activating nucleotidase; Provisional	83.77
COG2433	652	Uncharacterized conserved protein [Function unknow	83.75
PRK09039	343	hypothetical protein; Validated	83.73
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	83.72
PF05008	79	V-SNARE: Vesicle transport v-SNARE protein N-termi	83.6
PF14282	106	FlxA: FlxA-like protein	83.57
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	83.42
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	83.4
PRK14127	109	cell division protein GpsB; Provisional	83.36
PRK10803	263	tol-pal system protein YbgF; Provisional	83.25
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	82.99
COG3937	108	Uncharacterized conserved protein [Function unknow	82.98
PF11544	76	Spc42p: Spindle pole body component Spc42p; InterP	82.89
PF14988	206	DUF4515: Domain of unknown function (DUF4515)	82.71
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	82.42
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	82.4
PF00038	312	Filament: Intermediate filament protein; InterPro:	82.37
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	82.36
KOG3647	338	consensus Predicted coiled-coil protein [General f	82.33
PRK02119	73	hypothetical protein; Provisional	82.18
PF15397	258	DUF4618: Domain of unknown function (DUF4618)	82.17
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	82.15
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	82.01
COG2919	117	Septum formation initiator [Cell division and chro	82.0
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	81.75
PF13094	160	CENP-Q: CENP-Q, a CENPA-CAD centromere complex sub	81.7
PRK10803	263	tol-pal system protein YbgF; Provisional	81.68
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	81.63
TIGR02492	322	flgK_ends flagellar hook-associated protein FlgK.	81.59
PRK03992	389	proteasome-activating nucleotidase; Provisional	81.49
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	81.49
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	81.47
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	81.38
PF13815	118	Dzip-like_N: Iguana/Dzip1-like DAZ-interacting pro	81.28
PF12709	87	Kinetocho_Slk19: Central kinetochore-associated; I	81.15
KOG3433	203	consensus Protein involved in meiotic recombinatio	81.14
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	81.06
PRK04325	74	hypothetical protein; Provisional	81.02
COG5570	57	Uncharacterized small protein [Function unknown]	81.01
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	80.58
PF02388	406	FemAB: FemAB family; InterPro: IPR003447 The femAB	80.53
PRK04654	214	sec-independent translocase; Provisional	80.47
PF06103	90	DUF948: Bacterial protein of unknown function (DUF	80.45
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	80.41
KOG4343	655	consensus bZIP transcription factor ATF6 [Transcri	80.32
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	80.22
COG0497	557	RecN ATPase involved in DNA repair [DNA replicatio	80.14
PRK04406	75	hypothetical protein; Provisional	80.12

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

Probab=99.47  E-value=1.1e-13  Score=131.92  Aligned_cols=84  Identities=26%  Similarity=0.427  Sum_probs=66.8

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCC--CCCchhhHHHHHHHHHHHHHHHHHH---HHHHhHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRP--PKTDKATILSDAVQMMEQLRTEAQK---LKQSNENLQEKIKELKAE  149 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~--~K~dKasIL~dAIeYIk~Lq~qv~~---L~~e~~~L~~ei~eLk~E  149 (235)
                      ++.+|+++|||||++||++|.+|+.|||.+..  .|.+|.+||..+++||+.||+..++   ++.....|+..+++|...
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            56799999999999999999999999998743  5788999999999999999987663   333445566666666666


Q ss_pred             HHHHHHHHH
Q 026646          150 KNELRDEKQ  158 (235)
Q Consensus       150 knELr~E~~  158 (235)
                      +.||..+..
T Consensus       313 ieeLk~~~~  321 (411)
T KOG1318|consen  313 IEELKSEAG  321 (411)
T ss_pred             HHHHHHHHH
Confidence            666665443

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

Probab=99.47  E-value=6.3e-14  Score=97.68  Aligned_cols=51  Identities=37%  Similarity=0.530  Sum_probs=47.5

Q ss_pred             cCcchHHHHHHHHHHHHHHHHHHhcCCCC---CCCCCchhhHHHHHHHHHHHHH
Q 026646           76 SGSKACREKLRRDRLNERFLELGSMLEPG---RPPKTDKATILSDAVQMMEQLR  126 (235)
Q Consensus        76 ~~sH~~~ERrRRekINd~F~eLrslLP~~---~~~K~dKasIL~dAIeYIk~Lq  126 (235)
                      +.+|+.+||+||++||+.|.+|+.+||.+   ...|++|++||..||+||++||
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            45799999999999999999999999986   4589999999999999999997

; 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=99.45  E-value=1.2e-13  Score=96.39  Aligned_cols=55  Identities=35%  Similarity=0.437  Sum_probs=50.5

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCchhhHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGR-PPKTDKATILSDAVQMMEQLRTEA  129 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~-~~K~dKasIL~dAIeYIk~Lq~qv  129 (235)
                      .+.+|+.+||+||++||+.|.+|+++||... ..|++|++||..||+||+.|+.++
T Consensus         4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            4567999999999999999999999999873 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

>smart00353 HLH helix loop helix domain

Probab=99.43  E-value=3.7e-13  Score=92.38  Aligned_cols=51  Identities=39%  Similarity=0.490  Sum_probs=46.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCchhhHHHHHHHHHHHHHHHHH
Q 026646           80 ACREKLRRDRLNERFLELGSMLEPGR-PPKTDKATILSDAVQMMEQLRTEAQ  130 (235)
Q Consensus        80 ~~~ERrRRekINd~F~eLrslLP~~~-~~K~dKasIL~dAIeYIk~Lq~qv~  130 (235)
                      +..||+||++||+.|..|+++||.+. ..|.+|++||..||+||+.|+.+++
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            46899999999999999999999753 4899999999999999999998875

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=99.16  E-value=6.4e-11  Score=103.49  Aligned_cols=80  Identities=21%  Similarity=0.328  Sum_probs=70.0

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCC-----CCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRP-----PKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAE  149 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~-----~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~E  149 (235)
                      ++..|...||+||+.||.++..|..|||.+.+     .|+.||.||.++|+||.+|+.+..+-+++...|+.++..|+.=
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            45679999999999999999999999997643     3999999999999999999999999999999988888777766


Q ss_pred             HHHHH
Q 026646          150 KNELR  154 (235)
Q Consensus       150 knELr  154 (235)
                      +++..
T Consensus       142 k~~YE  146 (229)
T KOG1319|consen  142 KVNYE  146 (229)
T ss_pred             HHHHH
Confidence            65544

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

Probab=98.93  E-value=7.2e-09  Score=92.83  Aligned_cols=82  Identities=22%  Similarity=0.285  Sum_probs=68.0

Q ss_pred             ccCcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCc-hhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 026646           73 CCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTD-KATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKN  151 (235)
Q Consensus        73 ~~~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~d-KasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~Ekn  151 (235)
                      .+.+..|+.-||+||++|.+.|..|+.+||.+...+.. .++||.+|++||+.|+..........+.|..+-..|+.+.+
T Consensus        57 ~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~~e~~~l~~rl~  136 (232)
T KOG2483|consen   57 ASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLSRENRKLKARLE  136 (232)
T ss_pred             CcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35788999999999999999999999999998765555 69999999999999999888877777776666666665555


Q ss_pred             HHH
Q 026646          152 ELR  154 (235)
Q Consensus       152 ELr  154 (235)
                      +|.
T Consensus       137 ql~  139 (232)
T KOG2483|consen  137 QLS  139 (232)
T ss_pred             Hhc
Confidence            544

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

Probab=98.66  E-value=1.5e-08  Score=91.60  Aligned_cols=58  Identities=33%  Similarity=0.350  Sum_probs=50.9

Q ss_pred             ccCcCcchHHHHHHHHHHHHHHHHHHhcCCCC------CCCCCchhhHHHHHHHHHHHHHHHHH
Q 026646           73 CCVSGSKACREKLRRDRLNERFLELGSMLEPG------RPPKTDKATILSDAVQMMEQLRTEAQ  130 (235)
Q Consensus        73 ~~~~~sH~~~ERrRRekINd~F~eLrslLP~~------~~~K~dKasIL~dAIeYIk~Lq~qv~  130 (235)
                      +.++..|-..|||||++||..+.+|+.||+..      ...|++||.||+.|++|+++|+....
T Consensus        30 ~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   30 QYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             HHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            35677889999999999999999999999953      23799999999999999999998644

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.55  E-value=6.1e-08  Score=100.04  Aligned_cols=78  Identities=28%  Similarity=0.364  Sum_probs=70.6

Q ss_pred             ccCCcCCCCCccccCcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q 026646           61 EAGSRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQ  140 (235)
Q Consensus        61 E~~~~KR~R~es~~~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~  140 (235)
                      |+.+.||-+++ ..++.+||..|||-|..|||++.+|+.+||... .|..|.++|..||+||++|+...+.++.++..++
T Consensus       263 ek~Pi~rl~~G-~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~-aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~  340 (953)
T KOG2588|consen  263 EKKPIKRLLPG-GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTE-AKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR  340 (953)
T ss_pred             ccCchhhcCCC-CcccchhhHHHHHhhcchhHHHHHHHHhcCccH-hhhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence            35677777775 468999999999999999999999999999764 8999999999999999999999999999998887

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

Probab=98.43  E-value=2.6e-07  Score=94.72  Aligned_cols=53  Identities=30%  Similarity=0.419  Sum_probs=48.3

Q ss_pred             cCcchHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCchhhHHHHHHHHHHHHHHH
Q 026646           76 SGSKACREKLRRDRLNERFLELGSMLEPGR--PPKTDKATILSDAVQMMEQLRTE  128 (235)
Q Consensus        76 ~~sH~~~ERrRRekINd~F~eLrslLP~~~--~~K~dKasIL~dAIeYIk~Lq~q  128 (235)
                      +.+|+..||||||++|-.|.||+++||.+.  ..|+||.+||.+||.+|+.+++.
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            567999999999999999999999999763  26999999999999999998875

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.31  E-value=5.8e-07  Score=83.64  Aligned_cols=69  Identities=25%  Similarity=0.287  Sum_probs=59.1

Q ss_pred             cchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 026646           78 SKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKEL  146 (235)
Q Consensus        78 sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eL  146 (235)
                      --++.||||=.-||-+|..|++|||--...|.+||+||+.+.+||.+|.++--+|-..|.+|+..+.++
T Consensus        63 IANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn~elKr~~~E~  131 (373)
T KOG0561|consen   63 IANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQNGELKRLKLEE  131 (373)
T ss_pred             hhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccccccchHHHHHhhh
Confidence            356899999999999999999999976568999999999999999999998888877777766554443

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

Probab=97.79  E-value=6e-05  Score=68.83  Aligned_cols=61  Identities=25%  Similarity=0.297  Sum_probs=49.0

Q ss_pred             cCcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 026646           74 CVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQ  134 (235)
Q Consensus        74 ~~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~  134 (235)
                      .++..-..+||||=.|+|+.|..|+.---+.-+...-|+.||..||+||..||.-++++.+
T Consensus       117 DRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~  177 (284)
T KOG3960|consen  117 DRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQ  177 (284)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            4566666899999999999999998754333237899999999999999999876665443

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.61  E-value=0.00015  Score=56.56  Aligned_cols=56  Identities=23%  Similarity=0.389  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHHHhcCCCCCC----CCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 026646           87 RDRLNERFLELGSMLEPGRP----PKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEK  142 (235)
Q Consensus        87 RekINd~F~eLrslLP~~~~----~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~e  142 (235)
                      -|.||+.+..|+.+||..+.    .|..-+-+|++|+.||+.|+.+|..|.+.+.+|...
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            47899999999999998543    466667799999999999999999999998888654

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

Probab=97.53  E-value=0.0001  Score=64.98  Aligned_cols=60  Identities=22%  Similarity=0.251  Sum_probs=52.0

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGR--PPKTDKATILSDAVQMMEQLRTEAQKLKQ  134 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~--~~K~dKasIL~dAIeYIk~Lq~qv~~L~~  134 (235)
                      .+..++.+||.|=..+|..|.+||.+||...  ..|.+|+.+|.-||.||+.|+.-++.-+.
T Consensus       109 ~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~  170 (228)
T KOG4029|consen  109 QRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEA  170 (228)
T ss_pred             hhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhccccc
Confidence            4567778899999999999999999999764  47999999999999999999987665443

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=97.38  E-value=0.0017  Score=49.85  Aligned_cols=60  Identities=22%  Similarity=0.488  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      +..||+-|.=||-++++|+..|..|.+++..++....+|+.|+..||.|-...+.-|.++
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            567999999999999999999999999999999999999999999999998888877763

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.24  E-value=0.0033  Score=47.69  Aligned_cols=60  Identities=20%  Similarity=0.495  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      +..||+-|.=||-++++|++.|.+|.++..++......|+.|+..||.|-...+.-|+++
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            567999999999999999999999999999999999999999999999998888888764

>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=97.21  E-value=0.0037  Score=47.00  Aligned_cols=53  Identities=34%  Similarity=0.520  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      ++.+.+|..+++.+-..+..|+.++.+|+.+.+.|.+++..|+.+.++|+++-
T Consensus         3 ~E~l~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~   55 (72)
T PF06005_consen    3 LELLEQLEEKIQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQER   55 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555555555555555555555555555555555544443

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

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=97.09  E-value=0.00059  Score=67.43  Aligned_cols=68  Identities=32%  Similarity=0.415  Sum_probs=49.8

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCC-C-CCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPG-R-PPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELK  147 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~-~-~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk  147 (235)
                      ++..++.|||.|=..||+.|.||..+.-.- + .....|..||..||..|-.|++||.+     ..|.-+...||
T Consensus       526 RR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE-----RNLNPKaaclk  595 (632)
T KOG3910|consen  526 RRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE-----RNLNPKAACLK  595 (632)
T ss_pred             HHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH-----ccCChhhhhhh
Confidence            456677777777788999999999876421 0 13467899999999999999999865     23444455554

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

Probab=96.84  E-value=0.017  Score=43.40  Aligned_cols=57  Identities=28%  Similarity=0.471  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      +..||+-|.-|+.++++|+.+|..|.++...|+.+.+.|++|.......+..|=..|
T Consensus        13 i~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~~LL~kl   69 (72)
T PF06005_consen   13 IQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLRSLLGKL   69 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            467899999999999999999999887777777777777766665555554443333

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=96.62  E-value=0.014  Score=50.17  Aligned_cols=60  Identities=25%  Similarity=0.503  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHH---HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          115 LSDAVQMMEQLRTE---AQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       115 L~dAIeYIk~Lq~q---v~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      |.+.|.|+..|+..   .+.+..+++.|+.++.+|+.+...|..|+..|+.++..++...++|
T Consensus        82 l~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L  144 (161)
T TIGR02894        82 LQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTL  144 (161)
T ss_pred             HHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999874   6777888888888888888888888888888888887777776663

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.

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=96.43  E-value=0.021  Score=57.90  Aligned_cols=95  Identities=26%  Similarity=0.396  Sum_probs=71.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---cCCCCCCCC---CCCC
Q 026646          114 ILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM---SAPSGFLPH---PSSM  187 (235)
Q Consensus       114 IL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~---~~~p~~~p~---~~~~  187 (235)
                      |+...-.-+.+|+.+.++|..+.+++..+|++||+++..-+.|..+||.+||.-|.+++.+   +.|--|+|-   |..+
T Consensus        87 I~~sVs~EL~ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El~~~n~pkl~LP~sllP~~~  166 (907)
T KOG2264|consen   87 ILASVSLELTELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEELRETNNPKLFLPFSLLPLQI  166 (907)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHHHhhcCCceeeccccCcccC
Confidence            4555556688899999999999999999999999999999999999999999999999885   334445554   3344


Q ss_pred             chhhhhhhhhcCCccccccCC
Q 026646          188 SAAFAAQSQVAGNKLVPFIGY  208 (235)
Q Consensus       188 p~~~~~~~qa~~~k~~p~~~~  208 (235)
                      |+.--++.|+.+..|--...|
T Consensus       167 pr~l~pp~~~~~c~lhncfdy  187 (907)
T KOG2264|consen  167 PRELEPPSQISPCQLHNCFDY  187 (907)
T ss_pred             cccCCCccccCcccchhcccc
Confidence            544445556666655433344

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=95.95  E-value=0.12  Score=47.52  Aligned_cols=85  Identities=24%  Similarity=0.340  Sum_probs=63.1

Q ss_pred             ch-HHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 026646           79 KA-CREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEK  157 (235)
Q Consensus        79 H~-~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~  157 (235)
                      |. .-||.-|.||++|..+=-        ....|-+-..+-=..|++|..+.+.|..+|+.|+...+.|-.+.+||+.+.
T Consensus        63 HLS~EEK~~RrKLKNRVAAQt--------aRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~l  134 (292)
T KOG4005|consen   63 HLSWEEKVQRRKLKNRVAAQT--------ARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELDSEL  134 (292)
T ss_pred             ccCHHHHHHHHHHHHHHHHhh--------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence            44 578888889998876532        223344444444556888999999999999999988888888888888888


Q ss_pred             HHHHHHHHHHHHHH
Q 026646          158 QRLKADKEKLEQQV  171 (235)
Q Consensus       158 ~~Lk~e~e~le~ql  171 (235)
                      ..|+.++-.+.+|-
T Consensus       135 e~~~~~l~~~~~~~  148 (292)
T KOG4005|consen  135 ELLRQELAELKQQQ  148 (292)
T ss_pred             HHHHHHHHhhHHHH
Confidence            88888877776653

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=95.75  E-value=0.092  Score=40.45  Aligned_cols=56  Identities=29%  Similarity=0.424  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhc
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQR-------LKADKEKLEQQVKAM  174 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~-------Lk~e~e~le~qlk~~  174 (235)
                      .+.+.+|...|+..-.++.-|+.+|++||.+.+.|.+|...       |..+.+.|+++-.++
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            46788999999999999999999999999888888888766       555666666555543

>smart00338 BRLZ basic region leucin zipper

Probab=95.62  E-value=0.044  Score=39.36  Aligned_cols=40  Identities=28%  Similarity=0.476  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 026646          118 AVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEK  157 (235)
Q Consensus       118 AIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~  157 (235)
                      --.||..|+.+++.|+.+|..|..++..|..+...|++++
T Consensus        24 Kk~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~   63 (65)
T smart00338       24 KKAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL   63 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3458888888888888888888877777777666666543

>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=95.51  E-value=0.057  Score=38.72  Aligned_cols=35  Identities=31%  Similarity=0.593  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELR  154 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr  154 (235)
                      .||.+|+.++..|+.+|..|..++..|+.+...|.
T Consensus        26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~   60 (64)
T PF00170_consen   26 QYIEELEEKVEELESENEELKKELEQLKKEIQSLK   60 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45555555555555555555544444444433333

; 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=95.37  E-value=0.11  Score=41.85  Aligned_cols=51  Identities=29%  Similarity=0.481  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      |=.++..|++....|..++.+||....+|-+||+.|+-|.+.|...|....
T Consensus         6 l~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~   56 (107)
T PF06156_consen    6 LFDRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELE   56 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344555555566666666666666666666777777777777766666543

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

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=95.21  E-value=0.27  Score=48.75  Aligned_cols=56  Identities=20%  Similarity=0.401  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026646          121 MMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA  176 (235)
Q Consensus       121 YIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~  176 (235)
                      -+.+-|....+|+++++.|+.+.+.+.+...++......|++|+..|+.|++++..
T Consensus        70 ALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~  125 (475)
T PRK13729         70 ATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGA  125 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            34445556677777777777777777777777777778888888888888887544

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=94.97  E-value=0.016  Score=49.86  Aligned_cols=53  Identities=25%  Similarity=0.250  Sum_probs=46.6

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRT  127 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~  127 (235)
                      .+.-|+++||+|=-.||+.|..|+.++|..-..|.+|.--|.-|.+||-.|-+
T Consensus        78 qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~  130 (173)
T KOG4447|consen   78 QRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQ  130 (173)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhh
Confidence            34579999999999999999999999996544799999999999999998764

>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=94.77  E-value=0.24  Score=40.56  Aligned_cols=50  Identities=36%  Similarity=0.625  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          118 AVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKL  167 (235)
Q Consensus       118 AIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~l  167 (235)
                      .+..|.+|+.++..++.++..|+.++..|..+++++++|..+|-.+.+.+
T Consensus        14 ~~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~   63 (120)
T PF12325_consen   14 SVQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEEL   63 (120)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667777777777777777777777777777777777766655555544

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 [].

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=94.72  E-value=0.2  Score=40.55  Aligned_cols=50  Identities=22%  Similarity=0.371  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      |=.++..|++....+..++.+||....+|-+||+.|+.|.+.|...|..+
T Consensus         6 lfd~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~   55 (110)
T PRK13169          6 IFDALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEEL   55 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44455556666666666666666666677777777777777776666654

>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=94.69  E-value=0.22  Score=41.89  Aligned_cols=66  Identities=24%  Similarity=0.457  Sum_probs=52.8

Q ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhccC
Q 026646          110 DKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEK--NELRDEKQRLKADKEKLEQQVKAMSA  176 (235)
Q Consensus       110 dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~Ek--nELr~E~~~Lk~e~e~le~qlk~~~~  176 (235)
                      ++..+-.-..+ |.+|+.++..|+.++..|+.++..|....  .+|+.+...|+.+++.++..|..+..
T Consensus        70 s~eel~~ld~e-i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~  137 (169)
T PF07106_consen   70 SPEELAELDAE-IKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRS  137 (169)
T ss_pred             CchhHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33343333444 88899999999999999998888888876  58899999999999999999998755

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 [].

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.61  E-value=0.23  Score=44.02  Aligned_cols=78  Identities=12%  Similarity=0.101  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646           84 KLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKAD  163 (235)
Q Consensus        84 RrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e  163 (235)
                      |.|=.++...+.+|++-+-..          -...-+...+|++.++..++...+|+++.+.|+.+..+++.|+..|+++
T Consensus        92 ~~rlp~le~el~~l~~~l~~~----------~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~  161 (206)
T PRK10884         92 RTRVPDLENQVKTLTDKLNNI----------DNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQ  161 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH----------HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334467778888888666432          1222244444444444444444444444444444444444444444455


Q ss_pred             HHHHHHHH
Q 026646          164 KEKLEQQV  171 (235)
Q Consensus       164 ~e~le~ql  171 (235)
                      ++.++..+
T Consensus       162 ~~~~~~~~  169 (206)
T PRK10884        162 LDDKQRTI  169 (206)
T ss_pred             HHHHHHHH
Confidence            44444443

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

Probab=94.13  E-value=0.83  Score=42.47  Aligned_cols=14  Identities=21%  Similarity=0.423  Sum_probs=5.5

Q ss_pred             HHHHHHHHHHHHhc
Q 026646           87 RDRLNERFLELGSM  100 (235)
Q Consensus        87 RekINd~F~eLrsl  100 (235)
                      ...|...+..|+++
T Consensus       186 ~~~L~~e~~~Lk~~  199 (325)
T PF08317_consen  186 KAELEEELENLKQL  199 (325)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333334444443

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

Probab=94.09  E-value=0.037  Score=56.98  Aligned_cols=81  Identities=20%  Similarity=0.224  Sum_probs=66.6

Q ss_pred             cCcCcchHHHHHHHHHHHHHHHHHHhcCCCCC---CCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 026646           74 CVSGSKACREKLRRDRLNERFLELGSMLEPGR---PPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEK  150 (235)
Q Consensus        74 ~~~~sH~~~ERrRRekINd~F~eLrslLP~~~---~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~Ek  150 (235)
                      .+..+|...|.+||+.|.-.|..|.+++-..-   ..|+.+..-+..+++||..++.+...+.+|-..|+.++.+|++-+
T Consensus       650 ~r~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~~~lr~~~s~~~A~~  729 (856)
T KOG3582|consen  650 NRPITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAHSLRKEISELNAVI  729 (856)
T ss_pred             CCcccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhhhhhhhhhHHHHHHH
Confidence            57889999999999999999999998885321   258888888999999999999988888888888887777776665


Q ss_pred             HHHH
Q 026646          151 NELR  154 (235)
Q Consensus       151 nELr  154 (235)
                      +-++
T Consensus       730 ~~~~  733 (856)
T KOG3582|consen  730 SACQ  733 (856)
T ss_pred             HHhh
Confidence            5444

>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=94.03  E-value=0.51  Score=35.42  Aligned_cols=60  Identities=30%  Similarity=0.484  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      |..-=+-|.+|+.+-+.|....-.+.+.|+.|+....++..+...|+..++.++.++..+
T Consensus         7 l~EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l   66 (74)
T PF12329_consen    7 LAEKDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESL   66 (74)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334446788999999999988888888899998888888888888888888888877664

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.

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.01  E-value=0.27  Score=45.45  Aligned_cols=59  Identities=24%  Similarity=0.415  Sum_probs=29.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          113 TILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       113 sIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      +.|..+-.-.+.++.+++.|....+.++.++.+++.+.+++..|...|+.+|+.++..|
T Consensus        38 s~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I   96 (265)
T COG3883          38 SKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENI   96 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444445555555555555555555555555555555544444444444444433

>smart00787 Spc7 Spc7 kinetochore protein

Probab=93.95  E-value=0.77  Score=43.03  Aligned_cols=15  Identities=27%  Similarity=0.452  Sum_probs=6.2

Q ss_pred             HHHHHHHHHHHHhcC
Q 026646           87 RDRLNERFLELGSML  101 (235)
Q Consensus        87 RekINd~F~eLrslL  101 (235)
                      .+.|+..+..|+.+.
T Consensus       181 ~~~L~~e~~~L~~~~  195 (312)
T smart00787      181 KDALEEELRQLKQLE  195 (312)
T ss_pred             HHHHHHHHHHHHHhH
Confidence            334444444444433

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

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

Probab=93.77  E-value=0.5  Score=43.29  Aligned_cols=52  Identities=29%  Similarity=0.585  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      .+++...+++.++++.|..+..+|..+.++++++..+|..|+.+|+..++.+
T Consensus       138 ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l  189 (290)
T COG4026         138 EELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKL  189 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3455556667777888888888888888888888888888888888777764

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=93.67  E-value=0.49  Score=46.87  Aligned_cols=60  Identities=27%  Similarity=0.431  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH----------------------HHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKA----------------------EKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~----------------------EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      |..-|--+++|+.+++.|..+|+.|+.+.+.|++                      +...|.+|.+.|...+..|+.||+
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            3344555666777766666666666655555544                      444455555555555666666665


Q ss_pred             hc
Q 026646          173 AM  174 (235)
Q Consensus       173 ~~  174 (235)
                      .+
T Consensus       141 ~~  142 (472)
T TIGR03752       141 GV  142 (472)
T ss_pred             hc
Confidence            43

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=93.62  E-value=0.89  Score=43.49  Aligned_cols=60  Identities=12%  Similarity=0.200  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          114 ILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       114 IL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      -+.++...|..|..++..+..+...++.+|..+..+..+++.+...++.+++..+.+|+.
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            344455555555555566666666666666666666666666666666666666655555

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=93.59  E-value=0.58  Score=37.95  Aligned_cols=51  Identities=25%  Similarity=0.379  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      .+-|.+|.+++..|-.+...|+..+.+|-.|...|+-||..|+..+..+++
T Consensus         7 fd~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~   57 (110)
T PRK13169          7 FDALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA   57 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            345777888899999999999999999988888999999999988888744

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

Probab=93.56  E-value=0.56  Score=37.68  Aligned_cols=51  Identities=31%  Similarity=0.470  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      .+-|.+|.+++..|-.+...|+..+.+|-.|..+|+-||..|+..+..+++
T Consensus         7 ~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~   57 (107)
T PF06156_consen    7 FDRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ   57 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            345778889999999999999999999999999999999999998888877

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

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=93.50  E-value=0.63  Score=39.37  Aligned_cols=72  Identities=26%  Similarity=0.481  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCCCC
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPSS  186 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~~p~~~p~~~~  186 (235)
                      .+.++.-+..++.....+..++..+..++.........+|++...++.+.+++..+...+...-|.+..|..
T Consensus        72 ~~~~v~~L~h~keKl~~~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~~~~~~~l~~~~~~~~~P~l  143 (177)
T PF13870_consen   72 IGKTVQILTHVKEKLHFLSEELERLKQELKDREEELAKLREELYRVKKERDKLRKQNKKLRQQGGLLGVPAL  143 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcHH
Confidence            455677777777788888888888999999999999999999999999999999999998777776666543

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=93.47  E-value=0.75  Score=34.19  Aligned_cols=54  Identities=22%  Similarity=0.369  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      |.+|-...++|+.+|..|.++...+..|...|.+.+..-++.+|.+=..|++|-
T Consensus         9 le~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rvEamI~RLk~le   62 (65)
T TIGR02449         9 VEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKVEAMITRLKALE   62 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence            344445555666666666666666666666666666666666666666666553

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.

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.40  E-value=0.66  Score=35.35  Aligned_cols=51  Identities=31%  Similarity=0.448  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      .+.+.+|...++.--....-|+.+|++||.++|.|..|.+.+....+.|+.
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            456777888888777777778888888877777777776655554444443

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=93.39  E-value=0.078  Score=53.50  Aligned_cols=61  Identities=33%  Similarity=0.327  Sum_probs=44.3

Q ss_pred             CCcCCCCCccccCc----CcchHHHHHHHHHHHHHHHHHHhcCCCCCC--CCCchhhHHHHHHHHHH
Q 026646           63 GSRKRLRSESCCVS----GSKACREKLRRDRLNERFLELGSMLEPGRP--PKTDKATILSDAVQMME  123 (235)
Q Consensus        63 ~~~KR~R~es~~~~----~sH~~~ERrRRekINd~F~eLrslLP~~~~--~K~dKasIL~dAIeYIk  123 (235)
                      .+|||.|+...-+.    .++.-=-||-||+||--+.-|.+|||--..  .|.||.|||.=+|.|++
T Consensus         9 AsrkRrrp~qk~rpp~~a~tkSNPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen    9 ASRKRRRPLQKQRPPPKALTKSNPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             hhhhccCCccccCCCccccccCCcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            45666665432111    233334578899999999999999993211  79999999999999986

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.32  E-value=0.68  Score=42.82  Aligned_cols=61  Identities=21%  Similarity=0.454  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      +...=.-|..|+.+.+.++.+++.|..+|.++..+.++++.++..+++++++++.+|+.+.
T Consensus        33 i~~~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~   93 (265)
T COG3883          33 IQNQDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELK   93 (265)
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5556667888888888999999999999999989999999999999999999999988864

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

Probab=93.12  E-value=0.39  Score=43.68  Aligned_cols=52  Identities=23%  Similarity=0.484  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA  176 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~  176 (235)
                      +..|.++++..|.+|++++..+..++..|+.|...|+++..+|-.+++=+.+
T Consensus        84 VtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylqS  135 (248)
T PF08172_consen   84 VTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQS  135 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            5568888888888888888888889999999999999999999999998754

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

>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=92.80  E-value=1  Score=32.14  Aligned_cols=36  Identities=36%  Similarity=0.587  Sum_probs=18.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          136 NENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       136 ~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      .+.|+.++..|..+...|+.++..|+.++..|..++
T Consensus        28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~   63 (64)
T PF00170_consen   28 IEELEEKVEELESENEELKKELEQLKKEIQSLKSEN   63 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            344444455555555555555555555555555443

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

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=92.74  E-value=0.75  Score=39.74  Aligned_cols=57  Identities=26%  Similarity=0.376  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          117 DAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       117 dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ....-...|+.+.+.|+.++.+|+++++.|..|..+|..+...++.+-+-|-..|..
T Consensus        94 ~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~Im~R  150 (161)
T TIGR02894        94 TTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDIMDR  150 (161)
T ss_pred             hcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344456678888888888888888888888888888888888887777777666553

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.

>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=92.72  E-value=0.5  Score=32.52  Aligned_cols=40  Identities=28%  Similarity=0.555  Sum_probs=19.0

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          132 LKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       132 L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      |+...+.|...-..|+.+..-|..|+..|++++..|...+
T Consensus         3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl   42 (45)
T PF02183_consen    3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKL   42 (45)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3334444444444444444445555555555555554433

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

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

Probab=92.60  E-value=0.54  Score=38.11  Aligned_cols=44  Identities=30%  Similarity=0.434  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKL  167 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~l  167 (235)
                      +|-.||-+|+..++.|.+.+..+|.|.-.||.||+.|-+=|+.|
T Consensus        60 RlItQVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNL  103 (120)
T KOG3650|consen   60 RLITQVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENL  103 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHH
Confidence            34446666777777777777777777778888888887766654

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

Probab=92.60  E-value=0.94  Score=36.34  Aligned_cols=56  Identities=20%  Similarity=0.369  Sum_probs=34.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          113 TILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       113 sIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      -+++=+|+|+-..|+   .|...+..|+++++.+..+..+|+.+...++.++..+..++
T Consensus        62 rLaQl~ieYLl~~q~---~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~  117 (118)
T PF13815_consen   62 RLAQLSIEYLLHCQE---YLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKES  117 (118)
T ss_pred             HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            346668888876665   34444555566666666666666666666666666665554

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

Probab=92.56  E-value=1.1  Score=38.72  Aligned_cols=82  Identities=24%  Similarity=0.376  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646           85 LRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADK  164 (235)
Q Consensus        85 rRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~  164 (235)
                      +.|..+..++..+..-+-..       -..+..--.-|..|+.++..|+.++..|..++++...-...|+||...|..+.
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 RSKGELAQQLVELNDELQEL-------EKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQL  160 (194)
T ss_dssp             ---------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccchh-------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555555544211       12233334456667777777777777777777777777777777777777777


Q ss_pred             HHHHHHHHh
Q 026646          165 EKLEQQVKA  173 (235)
Q Consensus       165 e~le~qlk~  173 (235)
                      .-++.++..
T Consensus       161 ~~~e~k~~~  169 (194)
T PF08614_consen  161 NMLEEKLRK  169 (194)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            776666654

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.

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=92.39  E-value=0.79  Score=45.50  Aligned_cols=59  Identities=8%  Similarity=0.155  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      |...=.-..+|+++++.|+.+.+.+..+.+++..++++|.+|+..|+.+++.+-.++..
T Consensus        71 LteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~~~~~  129 (475)
T PRK13729         71 TTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGANPVT  129 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcCCCC
Confidence            44555566778888888888887777777788888889999999999998766666443

>PRK10884 SH3 domain-containing protein; Provisional

Probab=92.36  E-value=1.2  Score=39.43  Aligned_cols=29  Identities=14%  Similarity=0.196  Sum_probs=10.8

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          132 LKQSNENLQEKIKELKAEKNELRDEKQRL  160 (235)
Q Consensus       132 L~~e~~~L~~ei~eLk~EknELr~E~~~L  160 (235)
                      |+++|++|++++..++.+...|+.++..+
T Consensus       137 L~~~n~~L~~~l~~~~~~~~~l~~~~~~~  165 (206)
T PRK10884        137 LKEENQKLKNQLIVAQKKVDAANLQLDDK  165 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333333

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=92.26  E-value=1.3  Score=33.04  Aligned_cols=52  Identities=23%  Similarity=0.424  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHh
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEK-------NELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~Ek-------nELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      |..||.....+...++..+..++.|..|.       .....++..|+.|++.|..+|+.
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       34455677777777777777664

>PRK02119 hypothetical protein; Provisional

Probab=92.10  E-value=2.3  Score=31.87  Aligned_cols=54  Identities=13%  Similarity=0.161  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      +..+..++..|+....-+...|.+|....-+-+.+...|+.++..|.++|+.+.
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            345667777777777777777777777777777777888888888888888765

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=91.95  E-value=2.1  Score=36.04  Aligned_cols=53  Identities=23%  Similarity=0.418  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ..+|.++++ .+|+.++..|.++++.|+.|...++-|...++...++|..-.-+
T Consensus        68 CR~KRv~Qk-~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~~~~~~  120 (135)
T KOG4196|consen   68 CRVKRVQQK-HELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEALQNSAVS  120 (135)
T ss_pred             HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            345666643 56888888888888888888888888888888887777766543

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

Probab=91.94  E-value=0.74  Score=42.97  Aligned_cols=19  Identities=26%  Similarity=0.370  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHHHHHHHHHh
Q 026646          155 DEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       155 ~E~~~Lk~e~e~le~qlk~  173 (235)
                      +|...|+++++....+|..
T Consensus       113 ~e~~sl~~q~~~~~~~L~~  131 (314)
T PF04111_consen  113 EERDSLKNQYEYASNQLDR  131 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            4445556666666666555

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.

>PRK04406 hypothetical protein; Provisional

Probab=91.84  E-value=2.6  Score=31.84  Aligned_cols=52  Identities=17%  Similarity=0.183  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      .|..++..|+....-+...|++|....-+...+...|+.++..|..+|+.+.
T Consensus         8 ~le~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~~~   59 (75)
T PRK04406          8 QLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVKNMD   59 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            5667777777777777777777777777777777888888888888888765

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=91.84  E-value=3  Score=30.99  Aligned_cols=53  Identities=26%  Similarity=0.435  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      ++.|..++..|-...++|+.+...|+.+...++.|...|....+--.+.|++|
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            56788888888888888888888888888888888888888888888888776

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.

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=91.51  E-value=1.7  Score=32.37  Aligned_cols=54  Identities=17%  Similarity=0.358  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       116 ~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      ..+.+-+...+.....|..++......+...-.+.++|++|+..|+.|++.+..
T Consensus        15 d~~~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~~r~   68 (69)
T PF14197_consen   15 DSLTRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEELRA   68 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            345555555556666666777766667777777888888888888888776543

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

Probab=91.47  E-value=1.1  Score=41.64  Aligned_cols=7  Identities=29%  Similarity=0.586  Sum_probs=2.6

Q ss_pred             HHHhcCC
Q 026646           96 ELGSMLE  102 (235)
Q Consensus        96 eLrslLP  102 (235)
                      .|..++|
T Consensus       174 ~l~~~~~  180 (325)
T PF08317_consen  174 QLDELLP  180 (325)
T ss_pred             HHHHHHH
Confidence            3333333

>PRK11637 AmiB activator; Provisional

Probab=91.46  E-value=1.4  Score=42.13  Aligned_cols=31  Identities=35%  Similarity=0.443  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          142 KIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       142 ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      +|..+..+++++..+...+..++..++.+|.
T Consensus        90 ~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~  120 (428)
T PRK11637         90 KLRETQNTLNQLNKQIDELNASIAKLEQQQA  120 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333344444444444444444444

>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=91.43  E-value=2.2  Score=46.61  Aligned_cols=85  Identities=24%  Similarity=0.404  Sum_probs=51.8

Q ss_pred             HHHHHHHHHHhcCCCCCCCCCchh-hHHHHHHHHHHHHHHHHHHHHHH----------hHHHHHHHHHHHHHHHHHHHHH
Q 026646           89 RLNERFLELGSMLEPGRPPKTDKA-TILSDAVQMMEQLRTEAQKLKQS----------NENLQEKIKELKAEKNELRDEK  157 (235)
Q Consensus        89 kINd~F~eLrslLP~~~~~K~dKa-sIL~dAIeYIk~Lq~qv~~L~~e----------~~~L~~ei~eLk~EknELr~E~  157 (235)
                      .+++++.+|+..+|.... ...|. +=+...+.-|..|..++.+++..          ...+++.|.+++.|.+++.++.
T Consensus       803 ~~ee~~~~lr~~~~~l~~-~l~~~~~~~k~~~~~~~~l~~~i~~~E~~~~k~~~d~~~l~~~~~~ie~l~kE~e~~qe~~  881 (1293)
T KOG0996|consen  803 ELEERVRKLRERIPELEN-RLEKLTASVKRLAELIEYLESQIAELEAAVLKKVVDKKRLKELEEQIEELKKEVEELQEKA  881 (1293)
T ss_pred             HHHHHHHHHHHhhHHHHh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCcHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            366777778877775421 11221 11344555666666666666643          2345566888888888887554


Q ss_pred             HHHHHHHHHHHHHHHhcc
Q 026646          158 QRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       158 ~~Lk~e~e~le~qlk~~~  175 (235)
                      .. |++++.|+.++..++
T Consensus       882 ~K-k~~i~~lq~~i~~i~  898 (1293)
T KOG0996|consen  882 AK-KARIKELQNKIDEIG  898 (1293)
T ss_pred             hH-HHHHHHHHHHHHHhh
Confidence            45 788888877776653

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

Probab=91.38  E-value=0.88  Score=41.76  Aligned_cols=47  Identities=28%  Similarity=0.409  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      +.+++.+...|.++++.|+.+.+++..+...|+-|+++|.....+|.
T Consensus       144 l~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l~  190 (290)
T COG4026         144 LEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKLP  190 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhch
Confidence            33444444445555555544444444444444444444444433333

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

Probab=91.16  E-value=0.37  Score=41.70  Aligned_cols=20  Identities=45%  Similarity=0.675  Sum_probs=2.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 026646          151 NELRDEKQRLKADKEKLEQQ  170 (235)
Q Consensus       151 nELr~E~~~Lk~e~e~le~q  170 (235)
                      ..|+.++++||-|+-.|.++
T Consensus        27 E~L~~~~QRLkDE~RDLKqE   46 (166)
T PF04880_consen   27 ENLREEVQRLKDELRDLKQE   46 (166)
T ss_dssp             HHHHHCH-------------
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333

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.

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

Probab=91.03  E-value=2  Score=37.69  Aligned_cols=60  Identities=20%  Similarity=0.417  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          113 TILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       113 sIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      .|..+=++.|+.|+.++..++..-......+.++..|...|.+-...+..+++.|+.+|+
T Consensus        20 dIT~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~   79 (201)
T PF13851_consen   20 DITLNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLK   79 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            466677788888888887777554444444444444444444444444444444444443

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

Probab=90.92  E-value=2.5  Score=36.02  Aligned_cols=17  Identities=41%  Similarity=0.688  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 026646          154 RDEKQRLKADKEKLEQQ  170 (235)
Q Consensus       154 r~E~~~Lk~e~e~le~q  170 (235)
                      +.+...|+.|+++|+++
T Consensus        79 r~~~e~L~~eie~l~~~   95 (177)
T PF07798_consen   79 RSENEKLQREIEKLRQE   95 (177)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            33333333333333333

>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=90.75  E-value=1.4  Score=39.24  Aligned_cols=22  Identities=23%  Similarity=0.344  Sum_probs=9.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHh
Q 026646          152 ELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       152 ELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      .+......++.+++.|++++..
T Consensus        74 ~l~~~v~~q~~el~~L~~qi~~   95 (251)
T PF11932_consen   74 QLERQVASQEQELASLEQQIEQ   95 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333444444444444443

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.

>PHA02562 46 endonuclease subunit; Provisional

Probab=90.62  E-value=2.5  Score=40.99  Aligned_cols=77  Identities=16%  Similarity=0.232  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646           86 RRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKE  165 (235)
Q Consensus        86 RRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e  165 (235)
                      ++..+..++.+|+..+-..       -+-|...++-+..|+.++++|+.....+..+++.|..+.+++..++..+..++.
T Consensus       331 ~~~~~~~~i~el~~~i~~~-------~~~i~~~~~~~~~l~~ei~~l~~~~~~~~~~l~~l~~~l~~~~~~~~~~~ke~~  403 (562)
T PHA02562        331 EFNEQSKKLLELKNKISTN-------KQSLITLVDKAKKVKAAIEELQAEFVDNAEELAKLQDELDKIVKTKSELVKEKY  403 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhhhhchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666677776666422       122677888888899999999888888888888888888888888877777766


Q ss_pred             HHHH
Q 026646          166 KLEQ  169 (235)
Q Consensus       166 ~le~  169 (235)
                      ..+.
T Consensus       404 ~~~~  407 (562)
T PHA02562        404 HRGI  407 (562)
T ss_pred             HHHH
Confidence            6533

>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=90.54  E-value=3.8  Score=31.57  Aligned_cols=43  Identities=26%  Similarity=0.447  Sum_probs=22.3

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          131 KLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       131 ~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +|..+...||..+..|.....+.++|+..|++|.+-|+.=|..
T Consensus        20 ~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~n   62 (80)
T PF10224_consen   20 ELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGN   62 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444445555555555555555555555555555

The exact function is unknown.

>PRK00846 hypothetical protein; Provisional

Probab=90.46  E-value=3.7  Score=31.41  Aligned_cols=52  Identities=13%  Similarity=0.098  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      .|..++..|+....-....|++|....-+...+...|+.++..|..+|+.+.
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            4556666677666666666777777777777777788888888888888864

>smart00338 BRLZ basic region leucin zipper

Probab=90.37  E-value=2.9  Score=29.81  Aligned_cols=35  Identities=37%  Similarity=0.673  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          137 ENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       137 ~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      ..|+.++..|..+..+|+.+...|..++..|.+++
T Consensus        29 ~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~   63 (65)
T smart00338       29 EELERKVEQLEAENERLKKEIERLRRELEKLKSEL   63 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34444444444444444444444445544444443

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

Probab=90.34  E-value=5.1  Score=36.69  Aligned_cols=32  Identities=28%  Similarity=0.535  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELR  154 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr  154 (235)
                      .+++.++..|+.+|+.|+.++.+|++|...|+
T Consensus       218 ~e~~~r~~~leken~~lr~~v~~l~~el~~~~  249 (269)
T KOG3119|consen  218 DEMAHRVAELEKENEALRTQVEQLKKELATLR  249 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555555555555555554444444

>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=90.30  E-value=0.8  Score=31.90  Aligned_cols=30  Identities=30%  Similarity=0.574  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          140 QEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       140 ~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      .+.+.+|..+..+|..++..|..++..|+.
T Consensus        24 k~~~~~le~~~~~L~~en~~L~~~i~~L~~   53 (54)
T PF07716_consen   24 KQREEELEQEVQELEEENEQLRQEIAQLER   53 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            344455555555555555555555555544

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

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

Probab=90.27  E-value=1.1  Score=30.88  Aligned_cols=33  Identities=33%  Similarity=0.479  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          141 EKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       141 ~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ..-..|+...+.|+.++.+|+.|+++|..++..
T Consensus         5 ~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~   37 (45)
T PF02183_consen    5 RDYDALKASYDSLKAEYDSLKKENEKLRAEVQE   37 (45)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444455555555444444443

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

>TIGR02209 ftsL_broad cell division protein FtsL

Probab=90.24  E-value=2.6  Score=31.17  Aligned_cols=47  Identities=26%  Similarity=0.376  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      .+.+...+..+...++.+++.++.+.++|+.|...|.. .++++..-+
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~-~~rIe~~Ar   68 (85)
T TIGR02209        22 AQHQTRQLNNELQKLQLEIDKLQKEWRDLQLEVAELSR-HERIEKIAK   68 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-HHHHHHHHH
Confidence            44556666666777777777777777777777776644 566665544

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.

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

Probab=90.17  E-value=1.8  Score=35.46  Aligned_cols=50  Identities=20%  Similarity=0.327  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      .+-.++..|++....|..++..||+...+|-+||..|+-|.++|..-|..
T Consensus         5 eiFd~v~~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~   54 (114)
T COG4467           5 EIFDQVDNLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE   54 (114)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence            34456777788778888888888888889999999999999998887764

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

Probab=90.12  E-value=4.3  Score=38.51  Aligned_cols=64  Identities=25%  Similarity=0.396  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHHHhc--------CCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 026646           86 RRDRLNERFLELGSM--------LEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEK  150 (235)
Q Consensus        86 RRekINd~F~eLrsl--------LP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~Ek  150 (235)
                      |...++....+|--.        +++.. .+.+=+.+|.++-+-.+.|+.++..|++....++-+++.|+...
T Consensus        38 r~q~LKkk~~el~~~~~~~~d~~~~~~~-~~~~La~lL~~sre~Nk~L~~Ev~~Lrqkl~E~qGD~KlLR~~l  109 (319)
T PF09789_consen   38 RYQALKKKYRELIQEAAGFGDPSIPPEK-ENKNLAQLLSESREQNKKLKEEVEELRQKLNEAQGDIKLLREKL  109 (319)
T ss_pred             HHHHHHHHHHHhhhhhcccCCccCCccc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHH
Confidence            456666666666521        11121 33445677899999999999988888877666665555555533

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

Probab=90.10  E-value=2  Score=39.19  Aligned_cols=61  Identities=20%  Similarity=0.305  Sum_probs=52.6

Q ss_pred             CchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          109 TDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       109 ~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      .+-.+||.-.+.-=-+.++++.+|++++.++.+++..|+.|.+.|+.+|..|-..+--|+.
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            4567788877777778899999999999999999999999999999999999777766654

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

>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=90.10  E-value=1  Score=32.13  Aligned_cols=47  Identities=23%  Similarity=0.299  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      |..|+.-+.+|+.+.+.-..+......++.+|+.||..|++++++++
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            45566666677776655444556677888889999999999888765

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 [, ].

>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=90.03  E-value=1.6  Score=37.88  Aligned_cols=17  Identities=29%  Similarity=0.425  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 026646          156 EKQRLKADKEKLEQQVK  172 (235)
Q Consensus       156 E~~~Lk~e~e~le~qlk  172 (235)
                      |...||.+...|.++|+
T Consensus       171 ei~~lk~~~~ql~~~l~  187 (189)
T PF10211_consen  171 EIDFLKKQNQQLKAQLE  187 (189)
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            44444555555555544

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 [].

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

Probab=90.02  E-value=1.6  Score=41.94  Aligned_cols=29  Identities=48%  Similarity=0.538  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          145 ELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       145 eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      .|+.-.+||+.-++.|+.++++||+|+..
T Consensus       236 slkRt~EeL~~G~~kL~~~~etLEqq~~~  264 (365)
T KOG2391|consen  236 SLKRTEEELNIGKQKLVAMKETLEQQLQS  264 (365)
T ss_pred             HHHhhHHHHHhhHHHHHHHHHHHHHHHHH
Confidence            33333333444444444444444444333

>PRK04325 hypothetical protein; Provisional

Probab=89.96  E-value=4.5  Score=30.37  Aligned_cols=53  Identities=17%  Similarity=0.178  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      ..+..++.+|+....-++..|++|....-+-..+...|+.++..|..+|+.+.
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            34556666666666666666666666666666677777777777777777765

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=89.89  E-value=0.27  Score=48.41  Aligned_cols=46  Identities=26%  Similarity=0.435  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCC--CCCchhhHHHHHHHHHHHHHH
Q 026646           81 CREKLRRDRLNERFLELGSMLEPGRP--PKTDKATILSDAVQMMEQLRT  127 (235)
Q Consensus        81 ~~ERrRRekINd~F~eLrslLP~~~~--~K~dKasIL~dAIeYIk~Lq~  127 (235)
                      -.-|.||++-|--|.+|..+||-.+.  ...||++|+.=|..||| |+.
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            35689999999999999999996432  56999999999999998 443

>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=89.82  E-value=2.8  Score=37.84  Aligned_cols=20  Identities=25%  Similarity=0.338  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHHHHHhHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENL  139 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L  139 (235)
                      .+|.+++.+.+.|..|...+
T Consensus        32 ~~L~e~~kE~~~L~~Er~~h   51 (230)
T PF10146_consen   32 KCLEEYRKEMEELLQERMAH   51 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            44444444444444444333

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.

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

Probab=89.80  E-value=2.2  Score=31.34  Aligned_cols=51  Identities=18%  Similarity=0.281  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      |..++.+|+....-+...|++|....-+...+...|+.++..|..+|+.+.
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            455666666666666666666666666666677777777777777777765

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.

>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=89.71  E-value=1.4  Score=40.74  Aligned_cols=58  Identities=14%  Similarity=0.372  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCCC
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS-APSGFLP  182 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~-~~p~~~p  182 (235)
                      |+..++.+..+.++++..+..|..+...|.....+-++|+||.+..|+++. +.|.||.
T Consensus       167 l~~ai~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~vRPAfmd  225 (267)
T PF10234_consen  167 LKEAIKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERNQKRLQSLQSVRPAFMD  225 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHH
Confidence            444455555566666666666666767777777777888888888888874 4676664

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 [].

>TIGR02231 conserved hypothetical protein

Probab=89.62  E-value=2.4  Score=41.61  Aligned_cols=84  Identities=19%  Similarity=0.268  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHH---------------HHHHHHHhHHHHHHHHHHHHHHHH
Q 026646           88 DRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTE---------------AQKLKQSNENLQEKIKELKAEKNE  152 (235)
Q Consensus        88 ekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~q---------------v~~L~~e~~~L~~ei~eLk~EknE  152 (235)
                      ..|.+.+.+|..-+-..    .++...+...+.+|..+...               +.++.+-...+.+++.++..+..+
T Consensus        74 ~~l~~~l~~l~~~~~~~----~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (525)
T TIGR02231        74 AELRKQIRELEAELRDL----EDRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTEDRE  149 (525)
T ss_pred             HHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555544322    34566666666666666531               233444444445555666666666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcc
Q 026646          153 LRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       153 Lr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      |..+...|+.++.+|+.+|..++
T Consensus       150 ~~~~~~~~~~~l~~l~~~l~~l~  172 (525)
T TIGR02231       150 AERRIRELEKQLSELQNELNALL  172 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhc
Confidence            66666666666666666666543

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.

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

Probab=89.60  E-value=1.2  Score=37.39  Aligned_cols=53  Identities=26%  Similarity=0.528  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHhc
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEK--QRLKADKEKLEQQVKAM  174 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~--~~Lk~e~e~le~qlk~~  174 (235)
                      +..|..++..|+.++..|..+++.|+.|...|..+.  ..|..+++.|+.+++.+
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            455555555555555555555555555555554433  35555566666655554

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 [].

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

Probab=89.55  E-value=1.8  Score=36.58  Aligned_cols=21  Identities=29%  Similarity=0.327  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHhH
Q 026646          117 DAVQMMEQLRTEAQKLKQSNE  137 (235)
Q Consensus       117 dAIeYIk~Lq~qv~~L~~e~~  137 (235)
                      ....-.++|+.|+.+|++|..
T Consensus        37 ~~~~~~~~l~~Ei~~l~~E~~   57 (161)
T PF04420_consen   37 KSSKEQRQLRKEILQLKRELN   57 (161)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccHHHHHHHHHHHHHHHHHH
Confidence            344445556666666665554

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

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

Probab=89.30  E-value=0.3  Score=50.42  Aligned_cols=46  Identities=30%  Similarity=0.434  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCC--CCCCCchhhHHHHHHHHHHHHHH
Q 026646           81 CREKLRRDRLNERFLELGSMLEPG--RPPKTDKATILSDAVQMMEQLRT  127 (235)
Q Consensus        81 ~~ERrRRekINd~F~eLrslLP~~--~~~K~dKasIL~dAIeYIk~Lq~  127 (235)
                      -+-|-||.|=|+-|.+|..+||--  -....|||+|+.=||.|++ |+.
T Consensus        52 dAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR-lrk   99 (768)
T KOG3558|consen   52 DAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR-LRK   99 (768)
T ss_pred             hhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH-HHH
Confidence            466889999999999999999931  1268999999999999998 554

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

Probab=89.25  E-value=1.8  Score=31.15  Aligned_cols=43  Identities=40%  Similarity=0.600  Sum_probs=21.4

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          130 QKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       130 ~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      ..++.+...|+.+++.++.+..+|+.+...|+.+.+.++..-+
T Consensus        20 ~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~AR   62 (80)
T PF04977_consen   20 YQLNQEIAELQKEIEELKKENEELKEEIERLKNDPDYIEKVAR   62 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            3344444444444444555555555555555445555555544

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

>PRK00295 hypothetical protein; Provisional

Probab=89.24  E-value=5  Score=29.63  Aligned_cols=51  Identities=18%  Similarity=0.205  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      +..++.+|+....-+...|++|....-+...+...|+.++..|..+|+.+.
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            344555555555555555556655555666666666777777777777764

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

Probab=89.19  E-value=5  Score=36.21  Aligned_cols=93  Identities=28%  Similarity=0.294  Sum_probs=62.1

Q ss_pred             CcchHHHHHHHHHHHH----HHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 026646           77 GSKACREKLRRDRLNE----RFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNE  152 (235)
Q Consensus        77 ~sH~~~ERrRRekINd----~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknE  152 (235)
                      .-|...++..+.+=|+    .-..|+..+...  .|  ..+=..+..+=+..|+.+.++.+.+.+.++.+...|++...+
T Consensus       115 R~~~ll~~l~~l~~~~~~~~~~~~lk~~~~~~--~~--~~~~~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~  190 (216)
T KOG1962|consen  115 RLHTLLRELATLRANEKAMKENEALKKQLENS--SK--LEEENDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEG  190 (216)
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHhhhcc--cc--hhhhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555544322    222444444321  12  344445566667778888888888888888888888888888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q 026646          153 LRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       153 Lr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +.+|-.+|..|-.+|+.|+..
T Consensus       191 ~~~EydrLlee~~~Lq~~i~~  211 (216)
T KOG1962|consen  191 LQDEYDRLLEEYSKLQEQIES  211 (216)
T ss_pred             cccHHHHHHHHHHHHHHHHhc
Confidence            888888888888888888864

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

Probab=89.17  E-value=1.6  Score=42.05  Aligned_cols=39  Identities=15%  Similarity=0.318  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 026646          141 EKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSG  179 (235)
Q Consensus       141 ~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~~p~  179 (235)
                      .+++.|+.+..++.++...++.++++++.+|+.+.++|.
T Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (398)
T PTZ00454         29 KELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQSVPL   67 (398)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence            334444444444555555556666777777777777664

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

Probab=89.09  E-value=3.2  Score=32.18  Aligned_cols=51  Identities=31%  Similarity=0.546  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKA---EKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~---EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +.|+.+++.|..+...+..+|..++.   +..+|..+...++.++..++.+++.
T Consensus        39 r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~   92 (108)
T PF02403_consen   39 RELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKE   92 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555666666666566666655554   2345555666666666666655554

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 ....

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

Probab=88.99  E-value=0.27  Score=44.77  Aligned_cols=53  Identities=26%  Similarity=0.349  Sum_probs=45.0

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCchhhHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPG-RPPKTDKATILSDAVQMMEQLRT  127 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~-~~~K~dKasIL~dAIeYIk~Lq~  127 (235)
                      ++.+=|.+||.|=-.||+.|..||.+||.. ...|..|.-.|.-|-.||..|.+
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            456667899999999999999999999953 34899999999888888887764

>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=88.95  E-value=5.3  Score=32.77  Aligned_cols=48  Identities=19%  Similarity=0.284  Sum_probs=26.3

Q ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 026646          110 DKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEK  157 (235)
Q Consensus       110 dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~  157 (235)
                      .-++++..=-.-|+++..++..|+.++..|..+-+.+..|+-.|..++
T Consensus        13 ~~~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~   60 (120)
T PF12325_consen   13 PSVQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEEN   60 (120)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555555556666666666666665555555444444444444433

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 [].

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

Probab=88.90  E-value=4.4  Score=29.41  Aligned_cols=40  Identities=23%  Similarity=0.469  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLK  161 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk  161 (235)
                      |.+|-.+|+.|.....+|.+++..|+.+.....+|-.+-.
T Consensus         5 id~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN   44 (56)
T PF04728_consen    5 IDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARAN   44 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555555555555555555555544444444433

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.

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

Probab=88.81  E-value=2  Score=39.33  Aligned_cols=55  Identities=20%  Similarity=0.400  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      +|....++.+..++.+..+-+....++...+.+|..||..|+.+++.|++++..+
T Consensus       194 ~y~err~rNN~A~~kSR~~~k~~~~e~~~r~~~leken~~lr~~v~~l~~el~~~  248 (269)
T KOG3119|consen  194 EYKERRRRNNEAVRKSRDKRKQKEDEMAHRVAELEKENEALRTQVEQLKKELATL  248 (269)
T ss_pred             HHHHHHHhhhHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4655555555556655555555555566666666666666666666666666553

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

Probab=88.80  E-value=4.3  Score=34.21  Aligned_cols=39  Identities=33%  Similarity=0.559  Sum_probs=20.3

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          135 SNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       135 e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ++..|.+++..++.+.+.|+.|...++.+++.|.++++.
T Consensus        53 eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~   91 (140)
T PF10473_consen   53 EIETLEEELEELTSELNQLELELDTLRSEKENLDKELQK   91 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555555555555555555555554443

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

>PRK02793 phi X174 lysis protein; Provisional

Probab=88.75  E-value=6.5  Score=29.33  Aligned_cols=51  Identities=20%  Similarity=0.203  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      +..++.+|+....-+...|.+|....-+.+.+...|..++..|..+|+.+.
T Consensus         6 ~e~Ri~~LE~~lafQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   56 (72)
T PRK02793          6 LEARLAELESRLAFQEITIEELNVTVTAHEMEMAKLRDHLRLLTEKLKASQ   56 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            556666666666666666666766666667777777777888888887764

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

Probab=88.72  E-value=2.1  Score=33.92  Aligned_cols=52  Identities=25%  Similarity=0.396  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHhHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          122 MEQLRTEAQKLKQSNENL--QEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L--~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +..+..+++.++.+.+.|  ..++..|+.+..+++-+...+..+++.+.+++.-
T Consensus        44 ~~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~~~~~l   97 (106)
T PF10805_consen   44 LDEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVSHQLDL   97 (106)
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            344566666666666666  6667777777777777777777777777666553

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

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

Probab=88.62  E-value=0.77  Score=42.54  Aligned_cols=52  Identities=25%  Similarity=0.226  Sum_probs=44.1

Q ss_pred             cCcchHHHHHHHHHHHHHHHHHHhcCCCCCC-CCCchhhHHHHHHHHHHHHHH
Q 026646           76 SGSKACREKLRRDRLNERFLELGSMLEPGRP-PKTDKATILSDAVQMMEQLRT  127 (235)
Q Consensus        76 ~~sH~~~ERrRRekINd~F~eLrslLP~~~~-~K~dKasIL~dAIeYIk~Lq~  127 (235)
                      +..-+.+||+|=..||..|..|+.+||.+.. .|.+|-..|..|-.||--|-.
T Consensus       175 r~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~  227 (285)
T KOG4395|consen  175 RLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGC  227 (285)
T ss_pred             hcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHH
Confidence            4455689999999999999999999997543 688999999999999986653

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

Probab=88.54  E-value=3.9  Score=32.46  Aligned_cols=54  Identities=19%  Similarity=0.387  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKEL--KAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eL--k~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      +..|++++...+.....++++++.|  +.+.+.|+-+...++-++..++.+|+.++
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            3445555555566666666666666  66666677777777777777777776553

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

>TIGR00219 mreC rod shape-determining protein MreC

Probab=88.51  E-value=2.9  Score=38.45  Aligned_cols=41  Identities=20%  Similarity=0.329  Sum_probs=21.5

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          130 QKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       130 ~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      .+|++||++|++++.+|+.+.+.+   .+.|+.|.++|+..|..
T Consensus        69 ~~l~~EN~~Lr~e~~~l~~~~~~~---~~~l~~EN~rLr~LL~~  109 (283)
T TIGR00219        69 NNLEYENYKLRQELLKKNQQLEIL---TQNLKQENVRLRELLNS  109 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcC
Confidence            345566666666655553333322   22255666666665554

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.

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

Probab=88.47  E-value=3.7  Score=31.01  Aligned_cols=27  Identities=30%  Similarity=0.369  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKA  148 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~  148 (235)
                      +++...++.+|+.+|=.|.-+|..|..
T Consensus         2 lrEqe~~i~~L~KENF~LKLrI~fLee   28 (75)
T PF07989_consen    2 LREQEEQIDKLKKENFNLKLRIYFLEE   28 (75)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence            345556666666666555555544443

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

Probab=88.41  E-value=3.3  Score=31.92  Aligned_cols=49  Identities=29%  Similarity=0.394  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ  170 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~q  170 (235)
                      =.+|.+++..|+..+..|-..|..++.|-..|+.||..|..=|..|=..
T Consensus        18 k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm~~   66 (80)
T PF10224_consen   18 KEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLMSS   66 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3567888999999999999999999999999999999999888887444

The exact function is unknown.

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=88.33  E-value=4.2  Score=35.39  Aligned_cols=62  Identities=23%  Similarity=0.414  Sum_probs=50.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          112 ATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       112 asIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ..=|..++..+.+=+++...|.+-|.-|+++.+..+.....|.+++.+|..+-+++..+|..
T Consensus        59 s~dLe~~l~rLeEEqqR~~~L~qvN~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~eL~~  120 (182)
T PF15035_consen   59 SPDLEEALIRLEEEQQRSEELAQVNALLREQLEQARKANEALQEDLQKLTQDWERLRDELEQ  120 (182)
T ss_pred             cccHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34577788888888888889999999999998888888888898888888888887777654

>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=88.27  E-value=3.5  Score=35.23  Aligned_cols=29  Identities=34%  Similarity=0.452  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          140 QEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       140 ~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      .++++.|+.|..+...|...||.+.+.++
T Consensus       160 ~~ei~~lk~el~~~~~~~~~LkkQ~~~l~  188 (192)
T PF05529_consen  160 SEEIEKLKKELEKKEKEIEALKKQSEGLQ  188 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444444433

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

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=88.23  E-value=2.6  Score=37.83  Aligned_cols=39  Identities=28%  Similarity=0.549  Sum_probs=19.4

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          131 KLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       131 ~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +|.++|++|++++.+|+.+..+++    .|+.|.++|...|..
T Consensus        73 ~l~~en~~L~~e~~~l~~~~~~~~----~l~~en~~L~~lL~~  111 (276)
T PRK13922         73 DLREENEELKKELLELESRLQELE----QLEAENARLRELLNL  111 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHhcC
Confidence            444444444444444444443321    455666666666654

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=88.20  E-value=3.4  Score=36.67  Aligned_cols=47  Identities=23%  Similarity=0.425  Sum_probs=29.9

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026646          130 QKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA  176 (235)
Q Consensus       130 ~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~  176 (235)
                      ..|...+..+..+...|..+...|.+||..|..+.+.++.+.+.++.
T Consensus        84 ~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk~~~~eL~~  130 (193)
T PF14662_consen   84 RSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGLKKRSKELAT  130 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHH
Confidence            33334444445555666667777777777777777777777666543

>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=88.12  E-value=2.7  Score=30.22  Aligned_cols=32  Identities=34%  Similarity=0.425  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNEL  153 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknEL  153 (235)
                      +.+++++++.|+.++++++.+++.|+.++..|
T Consensus        19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l   50 (80)
T PF04977_consen   19 YYQLNQEIAELQKEIEELKKENEELKEEIERL   50 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34566666666666666666666666666666

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

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

Probab=87.96  E-value=2.3  Score=40.92  Aligned_cols=75  Identities=17%  Similarity=0.267  Sum_probs=54.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC--CCCCCCCCCCC
Q 026646          113 TILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA--PSGFLPHPSSM  187 (235)
Q Consensus       113 sIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~--~p~~~p~~~~~  187 (235)
                      +|+.++=..+.+|..-+..++++|..|+.++++++.|.+|-.+|.+.|..|....-.-...++.  +..|.+.+..+
T Consensus       120 ~vf~k~k~~~q~LE~li~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE~layqq~L~~eyQatf~eq~~ml  196 (401)
T PF06785_consen  120 EVFMKTKGDIQHLEGLIRHLREENQCLQLQLDALQQECGEKEEESQTLNRELAEALAYQQELNDEYQATFVEQHSML  196 (401)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhh
Confidence            4566666677788888889999999999999999999999999999887776553333333332  34566665544

>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=87.94  E-value=4.2  Score=38.78  Aligned_cols=43  Identities=16%  Similarity=0.330  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 026646          114 ILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDE  156 (235)
Q Consensus       114 IL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E  156 (235)
                      +|.-+++-+..|+.++..|..+++.|++++..+..+..++-.+
T Consensus       131 l~d~~l~~~~~l~~~~~~L~~enerL~~e~~~~~~qlE~~v~~  173 (342)
T PF06632_consen  131 LFDWCLDANSRLQAENEHLQKENERLESEANKLLKQLEKFVNA  173 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555666666777777777666666666655555555444433

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.

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

Probab=87.87  E-value=5  Score=39.45  Aligned_cols=15  Identities=33%  Similarity=0.295  Sum_probs=5.7

Q ss_pred             HHHHHHHHHHHHHHH
Q 026646          156 EKQRLKADKEKLEQQ  170 (235)
Q Consensus       156 E~~~Lk~e~e~le~q  170 (235)
                      .+..+...++.|+.|
T Consensus        95 ~I~~~~~~l~~l~~q  109 (420)
T COG4942          95 QIADLNARLNALEVQ  109 (420)
T ss_pred             hHHHHHHHHHHHHHH
Confidence            333333333444333

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

Probab=87.82  E-value=4.3  Score=41.37  Aligned_cols=60  Identities=28%  Similarity=0.436  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      ....-.-+.+|+.+++.|..+.+.+..+++.++.+..++.+|....+.+.++++.+++..
T Consensus       323 ~~~~~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~l~  382 (594)
T PF05667_consen  323 QEEQEQELEELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELKLK  382 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            446677888999999999999999999999999999999999999999999999998864

>PRK09039 hypothetical protein; Validated

Probab=87.78  E-value=3.9  Score=38.60  Aligned_cols=55  Identities=13%  Similarity=0.158  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          113 TILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKL  167 (235)
Q Consensus       113 sIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~l  167 (235)
                      ++..++-.-|..|++|++.|+.++..|+..|..++.+..+.+.....|+.+++..
T Consensus       130 ~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a  184 (343)
T PRK09039        130 QVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVA  184 (343)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445566667777788888887777777777666666555555555554444443

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

Probab=87.53  E-value=4.7  Score=37.68  Aligned_cols=6  Identities=50%  Similarity=0.291  Sum_probs=2.4

Q ss_pred             hhhhhh
Q 026646          192 AAQSQV  197 (235)
Q Consensus       192 ~~~~qa  197 (235)
                      ||-||+
T Consensus       173 AA~Gq~  178 (314)
T PF04111_consen  173 AAWGQT  178 (314)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            344433

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.

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

Probab=87.51  E-value=10  Score=31.14  Aligned_cols=10  Identities=30%  Similarity=0.620  Sum_probs=4.8

Q ss_pred             HHHHHHHHHH
Q 026646           89 RLNERFLELG   98 (235)
Q Consensus        89 kINd~F~eLr   98 (235)
                      -||..+..++
T Consensus         6 yiN~~L~s~G   15 (151)
T PF11559_consen    6 YINQQLLSRG   15 (151)
T ss_pred             HHHHHHHHCC
Confidence            3555555433

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.

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

Probab=87.20  E-value=4.6  Score=35.58  Aligned_cols=12  Identities=17%  Similarity=0.280  Sum_probs=4.9

Q ss_pred             HHHHHHHHHHHh
Q 026646          162 ADKEKLEQQVKA  173 (235)
Q Consensus       162 ~e~e~le~qlk~  173 (235)
                      .++...+.++..
T Consensus       126 ~~~~~~~~~l~~  137 (302)
T PF10186_consen  126 NELEERKQRLSQ  137 (302)
T ss_pred             HHHHHHHHHHHH
Confidence            334444444433

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

>PRK00736 hypothetical protein; Provisional

Probab=87.07  E-value=8.6  Score=28.37  Aligned_cols=49  Identities=12%  Similarity=0.224  Sum_probs=26.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          127 TEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       127 ~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      .++..|+....-+...|++|....-+-..+...|..++..|..+|+.+.
T Consensus         5 ~Ri~~LE~klafqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~~~   53 (68)
T PRK00736          5 ERLTELEIRVAEQEKTIEELSDQLAEQWKTVEQMRKKLDALTERFLSLE   53 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3444444444444444455544444555555666666666666666653

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=86.91  E-value=6.2  Score=33.23  Aligned_cols=30  Identities=33%  Similarity=0.621  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          144 KELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       144 ~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      .+|..++.+|..|...|+.|+.++..++.+
T Consensus        77 ~eLE~~k~~L~qqv~~L~~e~s~~~~E~da  106 (135)
T KOG4196|consen   77 HELEKEKAELQQQVEKLKEENSRLRRELDA  106 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555555555555555555555555444

>PHA03011 hypothetical protein; Provisional

Probab=86.90  E-value=7.2  Score=31.80  Aligned_cols=60  Identities=18%  Similarity=0.385  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      ...-++-+.+|..+-..|-++..-+..+++.+..=..+-.+|.-.|++|++||..++-.+
T Consensus        59 ~Nai~e~ldeL~~qYN~L~dEYn~i~Ne~k~~~~iIQdn~d~I~~LraeIDkLK~niaN~  118 (120)
T PHA03011         59 INAIIEILDELIAQYNELLDEYNLIENEIKDLEIIIQDNDDEIHFLRAEIDKLKENIANL  118 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHhcc
Confidence            344567777888888888888888888888888888888888889999999998887543

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

Probab=86.88  E-value=4  Score=39.09  Aligned_cols=21  Identities=10%  Similarity=0.150  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHhcCCCC
Q 026646           84 KLRRDRLNERFLELGSMLEPG  104 (235)
Q Consensus        84 RrRRekINd~F~eLrslLP~~  104 (235)
                      |.+=+.++..-..+.+.+|..
T Consensus       219 R~hleqm~~~~~~I~~~~~~~  239 (359)
T PF10498_consen  219 RSHLEQMKQHKKSIESALPET  239 (359)
T ss_pred             HHHHHHHHHHHHHHHHhhhHH
Confidence            444444444555555555543

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

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

Probab=86.48  E-value=5.8  Score=34.78  Aligned_cols=37  Identities=22%  Similarity=0.324  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRD  155 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~  155 (235)
                      .++.+.|..++.+-+.++.++.++|.+|+...-+|++
T Consensus       109 ~e~~k~le~~~~~~~~~~~~~e~~i~~Le~ki~el~~  145 (190)
T PF05266_consen  109 LEERKKLEKKIEEKEAELKELESEIKELEMKILELQR  145 (190)
T ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence            3344444444443333333444444444444444433

>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=86.48  E-value=8.1  Score=31.43  Aligned_cols=29  Identities=28%  Similarity=0.481  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 026646          117 DAVQMMEQLRTEAQKLKQSNENLQEKIKE  145 (235)
Q Consensus       117 dAIeYIk~Lq~qv~~L~~e~~~L~~ei~e  145 (235)
                      .+|.-|..|+.+...++.+...|+.+...
T Consensus        56 ~~~~~L~~lr~e~~~~~~~~~~l~~~~~~   84 (132)
T PF07926_consen   56 EDIKELQQLREELQELQQEINELKAEAES   84 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45666666666666666666655555433

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

>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=86.47  E-value=11  Score=27.67  Aligned_cols=54  Identities=28%  Similarity=0.463  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      |..=|+-=..|+.++.+.+..|..+..++++-.....+|..+...|+.+++.++
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            444455555667777777777777777777776666677777777766666554

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

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=86.45  E-value=2.8  Score=42.98  Aligned_cols=40  Identities=25%  Similarity=0.442  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 026646          118 AVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEK  157 (235)
Q Consensus       118 AIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~  157 (235)
                      -..-|+.|...+++|+.+|..|+.++.+|+.++.+|+++.
T Consensus       420 ~~~~i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l  459 (652)
T COG2433         420 YEKRIKKLEETVERLEEENSELKRELEELKREIEKLESEL  459 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444556666677777777777766666666666665543

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

Probab=86.44  E-value=6.7  Score=32.72  Aligned_cols=45  Identities=27%  Similarity=0.474  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          118 AVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKA  162 (235)
Q Consensus       118 AIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~  162 (235)
                      |++-+..|..++..|+.++..+..+|..|......|..+...+..
T Consensus        12 a~~r~e~~e~~~K~le~~~~~~E~EI~sL~~K~~~lE~eld~~~~   56 (143)
T PF12718_consen   12 AQDRAEELEAKVKQLEQENEQKEQEITSLQKKNQQLEEELDKLEE   56 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444445555555555555555555555554444444443333333

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 [].

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

Probab=86.21  E-value=6.2  Score=28.62  Aligned_cols=47  Identities=21%  Similarity=0.398  Sum_probs=39.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          127 TEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       127 ~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ..+.+|......|..++..|..+.+-||.+....|.|-.|-.+-|..
T Consensus         3 akid~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN   49 (56)
T PF04728_consen    3 AKIDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDN   49 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46788899999999999999999999999999888888877766654

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.

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=86.15  E-value=2.9  Score=33.24  Aligned_cols=43  Identities=26%  Similarity=0.431  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +|+++++.+++++++|       +.+...|+.|...|+...+-++.+.+.
T Consensus        31 ~l~~q~~~~~~e~~~l-------~~~n~~L~~eI~~L~~~~dyiEe~AR~   73 (105)
T PRK00888         31 RVNDQVAAQQQTNAKL-------KARNDQLFAEIDDLKGGQEAIEERARN   73 (105)
T ss_pred             HHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhhCcHHHHHHHHHH
Confidence            3444444444444444       444445555555555555666666655

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=86.11  E-value=2.7  Score=33.38  Aligned_cols=33  Identities=12%  Similarity=0.283  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          137 ENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       137 ~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      .++++++.+++.+..+|+.++..|+.|+++|+.
T Consensus        30 ~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~   62 (105)
T PRK00888         30 WRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG   62 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            344555555555666666666666666665544

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

Probab=86.08  E-value=4.1  Score=43.18  Aligned_cols=63  Identities=25%  Similarity=0.358  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026646          114 ILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA  176 (235)
Q Consensus       114 IL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~  176 (235)
                      |..+=-+.|++|..+.+.|++.+..|+.++++|..+..++-.+.+.|+.+.+.|+.||+-.+.
T Consensus       658 ~~~kyK~lI~~lD~~~e~lkQ~~~~l~~e~eeL~~~vq~~~s~hsql~~q~~~Lk~qLg~~~~  720 (970)
T KOG0946|consen  658 IQQKYKGLIRELDYQIENLKQMEKELQVENEELEEEVQDFISEHSQLKDQLDLLKNQLGIISS  720 (970)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccc
Confidence            344444555566666666666667777777777777777777888889999999999985433

>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=86.05  E-value=4.8  Score=40.81  Aligned_cols=7  Identities=29%  Similarity=0.857  Sum_probs=4.6

Q ss_pred             CCcCCCC
Q 026646           26 NFDWPSQ   32 (235)
Q Consensus        26 ~~~~~~~   32 (235)
                      +|.|...
T Consensus        55 Tf~Wa~~   61 (546)
T PF07888_consen   55 TFVWAPV   61 (546)
T ss_pred             eEEeecc
Confidence            5788653

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 [].

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=85.95  E-value=5.9  Score=35.55  Aligned_cols=46  Identities=26%  Similarity=0.406  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          114 ILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKAD  163 (235)
Q Consensus       114 IL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e  163 (235)
                      =.-+.+..+.+|+++.++|++++.+|+.++.++    +++++|+.+|+..
T Consensus        63 ~~~~~~~~~~~l~~en~~L~~e~~~l~~~~~~~----~~l~~en~~L~~l  108 (276)
T PRK13922         63 GVFESLASLFDLREENEELKKELLELESRLQEL----EQLEAENARLREL  108 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence            334445556667777777777777776665444    4555666666543

>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=85.82  E-value=9.9  Score=31.20  Aligned_cols=21  Identities=24%  Similarity=0.384  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhcC
Q 026646           81 CREKLRRDRLNERFLELGSML  101 (235)
Q Consensus        81 ~~ERrRRekINd~F~eLrslL  101 (235)
                      .++...|+.+++.+..|.+-+
T Consensus        48 ~r~~~~~e~l~~~~~~l~~d~   68 (151)
T PF11559_consen   48 DRDMEQREDLSDKLRRLRSDI   68 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHhHH
Confidence            466778888888887777654

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.

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

Probab=85.74  E-value=7  Score=32.93  Aligned_cols=57  Identities=21%  Similarity=0.456  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          117 DAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       117 dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ..-+-+..+....+.+.++...++.++.+++.+..+++.+...+..+...+++++..
T Consensus       127 ~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  183 (191)
T PF04156_consen  127 SVEERLDSLDESIKELEKEIRELQKELQDSREEVQELRSQLERLQENLQQLEEKIQE  183 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444444444444344444455555555555555555555555543

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 [].

>KOG4571 consensus Activating transcription factor 4 [Transcription]

Probab=85.73  E-value=9.6  Score=35.90  Aligned_cols=50  Identities=22%  Similarity=0.345  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          117 DAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       117 dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      -|++|=++=+.+-+.|..+       ++.|..+..+|++....|..||..|.+-|..
T Consensus       238 AAtRYRqKkRae~E~l~ge-------~~~Le~rN~~LK~qa~~lerEI~ylKqli~e  287 (294)
T KOG4571|consen  238 AATRYRQKKRAEKEALLGE-------LEGLEKRNEELKDQASELEREIRYLKQLILE  287 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5778866555554444444       4444455555555555666666666655543

>TIGR00219 mreC rod shape-determining protein MreC

Probab=85.65  E-value=3.2  Score=38.21  Aligned_cols=47  Identities=19%  Similarity=0.275  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          117 DAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEK  166 (235)
Q Consensus       117 dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~  166 (235)
                      +-+..+.+|++|.++|++++.+|+.+..   ....+|+.||.+|+..++-
T Consensus        63 ~~~~~~~~l~~EN~~Lr~e~~~l~~~~~---~~~~~l~~EN~rLr~LL~~  109 (283)
T TIGR00219        63 ENLKDVNNLEYENYKLRQELLKKNQQLE---ILTQNLKQENVRLRELLNS  109 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHhcC
Confidence            3344445577899999999888754433   3345578888888765443

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.

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=85.45  E-value=4.3  Score=37.58  Aligned_cols=90  Identities=29%  Similarity=0.326  Sum_probs=64.1

Q ss_pred             CCcCCCCCcccc------C-cCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHH
Q 026646           63 GSRKRLRSESCC------V-SGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQS  135 (235)
Q Consensus        63 ~~~KR~R~es~~------~-~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e  135 (235)
                      ..+||.|-..-+      + +.++.+.-.--||+=+.|+.++-..|              .|-++--..|+.+.+.|...
T Consensus        54 ~~rKr~RL~HLS~EEK~~RrKLKNRVAAQtaRDrKKaRm~eme~~i--------------~dL~een~~L~~en~~Lr~~  119 (292)
T KOG4005|consen   54 PKRKRRRLDHLSWEEKVQRRKLKNRVAAQTARDRKKARMEEMEYEI--------------KDLTEENEILQNENDSLRAI  119 (292)
T ss_pred             hHHHHHhhcccCHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHH
Confidence            356776654321      2 23333455556777777777776544              34455566789999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          136 NENLQEKIKELKAEKNELRDEKQRLKADKEK  166 (235)
Q Consensus       136 ~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~  166 (235)
                      |+.|..+.++|..+..++|+|...||.+..-
T Consensus       120 n~~L~~~n~el~~~le~~~~~l~~~~~~~~~  150 (292)
T KOG4005|consen  120 NESLLAKNHELDSELELLRQELAELKQQQQH  150 (292)
T ss_pred             HHHHHhhhHHHHHHHHHHHHHHHhhHHHHHH
Confidence            9999999999999999999999988876543

>smart00787 Spc7 Spc7 kinetochore protein

Probab=85.41  E-value=5.1  Score=37.60  Aligned_cols=6  Identities=0%  Similarity=0.235  Sum_probs=2.9

Q ss_pred             ccccCC
Q 026646           17 IVDDIP   22 (235)
Q Consensus        17 ~~~~~~   22 (235)
                      |+||+.
T Consensus        23 Fmdd~t   28 (312)
T smart00787       23 FMELLT   28 (312)
T ss_pred             eecccc
Confidence            455443

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

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

Probab=85.33  E-value=8.2  Score=39.02  Aligned_cols=81  Identities=19%  Similarity=0.244  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646           85 LRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADK  164 (235)
Q Consensus        85 rRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~  164 (235)
                      -=+..||+-|..|..+.-.-. .-.-|.+||++|-.....+...-..|+........+|...-.+.|.|=++...|..+|
T Consensus       108 sl~~~L~~ff~s~q~la~~P~-~~a~r~~vl~~a~~l~~~in~~~~~L~~l~~~i~~~I~~~V~~vNsLl~qIa~lN~qI  186 (552)
T COG1256         108 SLSTLLNDFFNSLQELASNPS-DTAARQAVLSKAQTLVNQINNTYEQLTDLRKDINAEIAATVDEVNSLLKQIADLNKQI  186 (552)
T ss_pred             cHHHHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345677888888887764221 3477888999998888888888777777766666676666666666665555555444


Q ss_pred             HH
Q 026646          165 EK  166 (235)
Q Consensus       165 e~  166 (235)
                      -+
T Consensus       187 ~~  188 (552)
T COG1256         187 RK  188 (552)
T ss_pred             HH
Confidence            43

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

Probab=85.16  E-value=5.5  Score=33.05  Aligned_cols=50  Identities=20%  Similarity=0.386  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +|.++++.|....++..+-++..+.+..+++++....+.+++.+++-+..
T Consensus        65 hLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv~~i~~dv~~v~~~V~~  114 (126)
T PF07889_consen   65 HLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDVSQIGDDVDSVQQMVEG  114 (126)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence            45566777776666666666667777777777777777777666655543

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

>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=85.10  E-value=1.6  Score=31.98  Aligned_cols=28  Identities=36%  Similarity=0.515  Sum_probs=15.2

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          135 SNENLQEKIKELKAEKNELRDEKQRLKA  162 (235)
Q Consensus       135 e~~~L~~ei~eLk~EknELr~E~~~Lk~  162 (235)
                      +.+.|+++|.+|....++|..||..||+
T Consensus        15 EVevLK~~I~eL~~~n~~Le~EN~~Lk~   42 (59)
T PF01166_consen   15 EVEVLKEQIAELEERNSQLEEENNLLKQ   42 (59)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4445555555555555555555555543

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.

>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=85.00  E-value=8.7  Score=31.38  Aligned_cols=61  Identities=28%  Similarity=0.418  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026646          116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA  176 (235)
Q Consensus       116 ~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~  176 (235)
                      ......+..|..++..|-+.|-.++.++..++.+..++.++...|+.+-..+++++..+..
T Consensus        30 ~~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~~k~~~~~~l~~   90 (150)
T PF07200_consen   30 QELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQEKEQQQDELSS   90 (150)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            3444445556666666666666667777888888888888888888888888888887743

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.

>KOG4797 consensus Transcriptional regulator [Transcription]

Probab=84.98  E-value=3.2  Score=34.13  Aligned_cols=48  Identities=23%  Similarity=0.351  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADK  164 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~  164 (235)
                      +..|.+.+|.=-  .=...+|.+-|+++|++|....+.|+.||..||.-.
T Consensus        50 IeQAMDLVKtHL--mfAVREEVe~Lk~qI~eL~er~~~Le~EN~lLk~~~   97 (123)
T KOG4797|consen   50 IEQAMDLVKTHL--MFAVREEVEVLKEQIRELEERNSALERENSLLKTLA   97 (123)
T ss_pred             HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            445666655311  112345666778888888877888888888887654

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

Probab=84.91  E-value=7  Score=34.28  Aligned_cols=46  Identities=28%  Similarity=0.428  Sum_probs=18.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          127 TEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       127 ~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      .++.+|+....+|+.+...++.++.....|..+|+++.+.+++++.
T Consensus       131 ~~i~~Le~ki~el~~~~~~~~~~ke~~~~ei~~lks~~~~l~~~~~  176 (190)
T PF05266_consen  131 SEIKELEMKILELQRQAAKLKEKKEAKDKEISRLKSEAEALKEEIE  176 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444443333333333333444444444444444443

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

Probab=84.90  E-value=5.4  Score=34.35  Aligned_cols=46  Identities=24%  Similarity=0.442  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      ++|..+++.+...++.|+.++..|..+.|-+.+....|+.|...|-
T Consensus       133 ~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l~~En~~Lv  178 (194)
T PF08614_consen  133 KDLEEELKEKNKANEILQDELQALQLQLNMLEEKLRKLEEENRELV  178 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444555555556666666666666666666666666665553

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.

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

Probab=84.81  E-value=2.9  Score=40.19  Aligned_cols=54  Identities=20%  Similarity=0.292  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       116 ~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      +.+.--.+.|.....+|+.++..|+.++++++.+.+.++.|...++.+++++..
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (398)
T PTZ00454         11 SSTTHTERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQS   64 (398)
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            333444556666677777777888888888888888888888888888888754

>PF15458 NTR2: Nineteen complex-related protein 2

Probab=84.58  E-value=12  Score=33.98  Aligned_cols=19  Identities=16%  Similarity=0.384  Sum_probs=14.0

Q ss_pred             cchHHHHHHHHHHHHHHHH
Q 026646           78 SKACREKLRRDRLNERFLE   96 (235)
Q Consensus        78 sH~~~ERrRRekINd~F~e   96 (235)
                      ......++||..|-+.+..
T Consensus       142 a~~~~~~~rR~~i~e~I~~  160 (254)
T PF15458_consen  142 AEREQKRRRREEIEEAIND  160 (254)
T ss_pred             HHHHHHHHHHHHHHHHHHh
Confidence            3445677788888888877

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=84.58  E-value=8.3  Score=34.31  Aligned_cols=61  Identities=30%  Similarity=0.399  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          114 ILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       114 IL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      ++..|++.=+-|..+++.|+.....|+++.+.|-++-..+..|++.|-++++.|+.+-..+
T Consensus        54 s~Qqal~~aK~l~eEledLk~~~~~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl  114 (193)
T PF14662_consen   54 SLQQALQKAKALEEELEDLKTLAKSLEEENRSLLAQARQLEKEQQSLVAEIETLQEENGKL  114 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence            4456666666666666666666666666666666666666666666666666666665543

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

Probab=84.57  E-value=10  Score=31.95  Aligned_cols=15  Identities=33%  Similarity=0.419  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHhcCC
Q 026646           88 DRLNERFLELGSMLE  102 (235)
Q Consensus        88 ekINd~F~eLrslLP  102 (235)
                      +.|.+++..|-.=|.
T Consensus        20 dsle~~v~~LEreLe   34 (140)
T PF10473_consen   20 DSLEDHVESLERELE   34 (140)
T ss_pred             hhHHHHHHHHHHHHH
Confidence            445555555555443

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

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

Probab=84.48  E-value=9  Score=32.28  Aligned_cols=88  Identities=19%  Similarity=0.359  Sum_probs=40.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHH----HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 026646           80 ACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAV----QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRD  155 (235)
Q Consensus        80 ~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAI----eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~  155 (235)
                      ....+.+-..+.+.+.++...+-..    .....-+.+..    +..+..+.+++.++.....+.+++.++..+..+.++
T Consensus        83 ~~~~~~~l~~l~~el~~l~~~~~~~----~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~  158 (191)
T PF04156_consen   83 LSELQQQLQQLQEELDQLQERIQEL----ESELEKLKEDLQELRELLKSVEERLDSLDESIKELEKEIRELQKELQDSRE  158 (191)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344555555566666655555311    11222222222    222244444444555555555555555544444445


Q ss_pred             HHHHHHHHHHHHHHHH
Q 026646          156 EKQRLKADKEKLEQQV  171 (235)
Q Consensus       156 E~~~Lk~e~e~le~ql  171 (235)
                      +...++.+..++++..
T Consensus       159 ~~~~~~~~~~~~~~~~  174 (191)
T PF04156_consen  159 EVQELRSQLERLQENL  174 (191)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            5555555555554443

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 [].

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

Probab=84.26  E-value=3.9  Score=29.57  Aligned_cols=34  Identities=15%  Similarity=0.392  Sum_probs=13.7

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          131 KLKQSNENLQEKIKELKAEKNELRDEKQRLKADK  164 (235)
Q Consensus       131 ~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~  164 (235)
                      +|+.+...+...+.-++.|.++++++...++..+
T Consensus         4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~env   37 (55)
T PF05377_consen    4 ELENELPRIESSINTVKKENEEISESVEKIEENV   37 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333443334444444444444444443333

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

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

Probab=83.98  E-value=6.7  Score=35.44  Aligned_cols=28  Identities=32%  Similarity=0.462  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEK  142 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~e  142 (235)
                      +..+-+=++.++.+++.|..+...|+.+
T Consensus       211 ~~~~~~E~~~~r~~~~~l~~el~~l~~~  238 (312)
T PF00038_consen  211 LESAKEELKELRRQIQSLQAELESLRAK  238 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhHhHHHHHHhhhhHhhhhhhccccc
Confidence            3333344444444444444433333333

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 ....

>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=83.86  E-value=0.62  Score=36.84  Aligned_cols=49  Identities=31%  Similarity=0.568  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADK  164 (235)
Q Consensus       116 ~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~  164 (235)
                      .+.=+||..|..++..|..++..|+.++..|..+..+++.....|+..+
T Consensus        21 ~eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~~~l   69 (131)
T PF05103_consen   21 DEVDDFLDELAEELERLQRENAELKEEIEELQAQLEELREEEESLQRAL   69 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT---------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHhh
Confidence            3455788888888888888888877777777666666665555554443

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.

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=83.77  E-value=3.8  Score=38.90  Aligned_cols=48  Identities=21%  Similarity=0.497  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCC
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS  178 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~~p  178 (235)
                      .|...+.+++.++++|+.++++|       ..+...++.++++++.+++.+..+|
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~   52 (389)
T PRK03992          5 ALEERNSELEEQIRQLELKLRDL-------EAENEKLERELERLKSELEKLKSPP   52 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHhhCCC
Confidence            34444445544555554444444       4444455566666666666665554

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=83.75  E-value=4.5  Score=41.54  Aligned_cols=40  Identities=28%  Similarity=0.474  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELR  154 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr  154 (235)
                      +.+--+-++.|+.+++.|+.++++++.+|..|+.+..+++
T Consensus       424 i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~  463 (652)
T COG2433         424 IKKLEETVERLEEENSELKRELEELKREIEKLESELERFR  463 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445666666666666666666666666655554443

>PRK09039 hypothetical protein; Validated

Probab=83.73  E-value=7.5  Score=36.71  Aligned_cols=49  Identities=14%  Similarity=0.219  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      .+.+|..|..+.+.|+.++..|..++..+..+....+.+++.|++.|..
T Consensus       135 ~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~  183 (343)
T PRK09039        135 ALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNV  183 (343)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555555555555555555555566665555544

>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=83.72  E-value=8.5  Score=36.75  Aligned_cols=38  Identities=18%  Similarity=0.344  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 026646          121 MMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQ  158 (235)
Q Consensus       121 YIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~  158 (235)
                      -+.+|+.+.++|+.+..++..+++++..+|.++..+.-
T Consensus       145 ~~~~L~~enerL~~e~~~~~~qlE~~v~~K~~~E~~L~  182 (342)
T PF06632_consen  145 ENEHLQKENERLESEANKLLKQLEKFVNAKEEHEEDLY  182 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34467888888999888898888888888888877653

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.

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

Probab=83.60  E-value=5.9  Score=28.91  Aligned_cols=58  Identities=10%  Similarity=0.332  Sum_probs=36.3

Q ss_pred             CchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          109 TDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       109 ~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      .+|-..|.++-.+|.+...-+.+|+-|...+..      .+++.+.......++++.+|+.+|+
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            577777777777777777777777766655532      3344455555555566666666554

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.

>PF14282 FlxA: FlxA-like protein

Probab=83.57  E-value=6.9  Score=31.02  Aligned_cols=55  Identities=20%  Similarity=0.309  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEK----IKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~e----i~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      -..|+.|+.+++.|.+++..|...    .+.-......|..+...|.++|-.++.+...
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            566777777777777777766552    1222333334555555555555555555433

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=83.42  E-value=9.4  Score=39.86  Aligned_cols=8  Identities=25%  Similarity=0.426  Sum_probs=4.4

Q ss_pred             cccccCCC
Q 026646           44 SVTIDCSF   51 (235)
Q Consensus        44 ~~~~~~~~   51 (235)
                      .|..||..
T Consensus       641 ~vTldG~~  648 (1164)
T TIGR02169       641 MVTLEGEL  648 (1164)
T ss_pred             EEEeCcee
Confidence            45666554

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.

>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=83.40  E-value=9.4  Score=31.05  Aligned_cols=40  Identities=33%  Similarity=0.421  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADK  164 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~  164 (235)
                      |+..++.|..++..+...+.+|.+++++++.....-|..+
T Consensus        42 L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le~eK~ak   81 (107)
T PF09304_consen   42 LRNALQSLQAQNASRNQRIAELQAKIDEARRNLEDEKQAK   81 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555566666666666667777777777665444333333

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.

>PRK14127 cell division protein GpsB; Provisional

Probab=83.36  E-value=7.6  Score=31.48  Aligned_cols=28  Identities=39%  Similarity=0.582  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          146 LKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       146 Lk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      |..|..+|++++..|+.++..++.++..
T Consensus        42 l~~e~~~Lk~e~~~l~~~l~e~~~~~~~   69 (109)
T PRK14127         42 FQKEIEELQQENARLKAQVDELTKQVSV   69 (109)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            3334444444555555555555555554

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=83.25  E-value=6.6  Score=35.67  Aligned_cols=50  Identities=14%  Similarity=0.251  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      +-+|+++++.|+.++.+|+=+|+++.-+.+++.+.-..+..+++++-.++
T Consensus        56 ~~~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~dld~r~~~~  105 (263)
T PRK10803         56 LTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDSLSSGG  105 (263)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            34566666666666666666666666666666665556666666654433

>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=82.99  E-value=9.3  Score=31.08  Aligned_cols=38  Identities=16%  Similarity=0.240  Sum_probs=18.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          128 EAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKE  165 (235)
Q Consensus       128 qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e  165 (235)
                      +.+.|+..+..|+.+-..+...+++|+.+...+...++
T Consensus        38 qkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le   75 (107)
T PF09304_consen   38 QKDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLE   75 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444445555545555555555555444444443

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.

>COG3937 Uncharacterized conserved protein [Function unknown]

Probab=82.98  E-value=9  Score=31.21  Aligned_cols=58  Identities=22%  Similarity=0.391  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHh-HHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHH
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSN-ENLQEKIKELKAEK--------NELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~-~~L~~ei~eLk~Ek--------nELr~E~~~Lk~e~e~le~qlk  172 (235)
                      ...|-+|+.+|-++.+.-+.+. ++++.+|+.+....        .+|+.+...|+.++-.|+.+++
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            4678889998888877544433 23455555554444        3566666666666666666654

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

Probab=82.89  E-value=8.4  Score=29.57  Aligned_cols=44  Identities=25%  Similarity=0.326  Sum_probs=19.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          127 TEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ  170 (235)
Q Consensus       127 ~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~q  170 (235)
                      ++..+|+..+...+++|..|+.=...||.....+..-..+|+.+
T Consensus         5 ~qNk~L~~kL~~K~eEI~rLn~lv~sLR~KLiKYt~LnkkLq~~   48 (76)
T PF11544_consen    5 KQNKELKKKLNDKQEEIDRLNILVGSLRGKLIKYTELNKKLQDQ   48 (76)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444444443333344433

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

>PF14988 DUF4515: Domain of unknown function (DUF4515)

Probab=82.71  E-value=11  Score=33.44  Aligned_cols=46  Identities=26%  Similarity=0.468  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ  170 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~q  170 (235)
                      |-.-...+..+|..|+.++.+|..+...|+..+..|..++..|.++
T Consensus       154 l~e~~~~i~~EN~~L~k~L~~l~~e~~~L~~~~~~Le~qk~~L~~e  199 (206)
T PF14988_consen  154 LDEFTRSIKRENQQLRKELLQLIQEAQKLEARKSQLEKQKQQLQQE  199 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555566666666555555555655555555555555444

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

Probab=82.42  E-value=8.3  Score=33.56  Aligned_cols=17  Identities=24%  Similarity=0.487  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 026646          156 EKQRLKADKEKLEQQVK  172 (235)
Q Consensus       156 E~~~Lk~e~e~le~qlk  172 (235)
                      ++..|+.++..|+.+|.
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 [].

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

Probab=82.40  E-value=5  Score=28.99  Aligned_cols=37  Identities=22%  Similarity=0.505  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          137 ENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       137 ~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ..|+.++..+....+-+|.|++.++.+++++++-++-
T Consensus         3 ~elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~   39 (55)
T PF05377_consen    3 DELENELPRIESSINTVKKENEEISESVEKIEENVKD   39 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566666677777777777777777777777776665

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

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

Probab=82.37  E-value=32  Score=31.08  Aligned_cols=16  Identities=19%  Similarity=0.466  Sum_probs=6.5

Q ss_pred             HHHHHHHHHHHHHHhH
Q 026646          122 MEQLRTEAQKLKQSNE  137 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~  137 (235)
                      |.+|+.++..+..++.
T Consensus        56 l~~lr~~id~~~~eka   71 (312)
T PF00038_consen   56 LRELRRQIDDLSKEKA   71 (312)
T ss_dssp             HHCHHHHHHHHHHHHH
T ss_pred             HHHhHHhhhhHHHHhh
Confidence            3444444444433333

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 ....

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

Probab=82.36  E-value=7.6  Score=28.50  Aligned_cols=49  Identities=18%  Similarity=0.297  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      +.|.+|+.++.-++...++|...+-....++..|+.+...|...+..++
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            3455566666666666666666665555666666666666655555554

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.

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

Probab=82.33  E-value=4.8  Score=37.89  Aligned_cols=59  Identities=14%  Similarity=0.322  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC-CCCCCCC
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA-PSGFLPH  183 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~-~p~~~p~  183 (235)
                      |+..++....+.+++..+++-++.+.++|.....+-|.|.|++++-|.++.+ .|+||..
T Consensus       110 lk~aIq~i~~~~q~~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRle~LqsiRP~~MdE  169 (338)
T KOG3647|consen  110 LKSAIQAIQVRLQSSRAQLNNVASDEAALGSKIERRKAELERTRKRLEALQSIRPAHMDE  169 (338)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHH
Confidence            4444555555555666666666667777777777888888888888888754 6766654

>PRK02119 hypothetical protein; Provisional

Probab=82.18  E-value=14  Score=27.64  Aligned_cols=53  Identities=8%  Similarity=0.113  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       116 ~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      ...-+.|.+|+.++.-++...+.|...+-....++..|+.+...|...+..++
T Consensus         5 ~~~e~Ri~~LE~rla~QE~tie~LN~~v~~Qq~~id~L~~ql~~L~~rl~~~~   57 (73)
T PRK02119          5 QNLENRIAELEMKIAFQENLLEELNQALIEQQFVIDKMQVQLRYMANKLKDMQ   57 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            33445677788888777777777777777777777777777777766555544

>PF15397 DUF4618: Domain of unknown function (DUF4618)

Probab=82.17  E-value=6.8  Score=36.18  Aligned_cols=83  Identities=27%  Similarity=0.329  Sum_probs=50.6

Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHH-HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646           88 DRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQ-LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEK  166 (235)
Q Consensus        88 ekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~-Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~  166 (235)
                      +.+++.+...+.-+...  -...|-.||+.++.-+.. .+..+-..-..|..++.++..-+.++++|.++...|+++++.
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 DELNEMRQMELASLSRK--IQEKKEEILSSAAEKTQSPMQPALLQRTLENQVMQKEIVQFREEIDELEEEIPQLRAEVEQ  218 (258)
T ss_pred             HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455444444444322  345667788876655444 444444445566667777766677777777777777777777


Q ss_pred             HHHHHH
Q 026646          167 LEQQVK  172 (235)
Q Consensus       167 le~qlk  172 (235)
                      |..+..
T Consensus       219 L~~~~~  224 (258)
T PF15397_consen  219 LQAQAQ  224 (258)
T ss_pred             HHHhhc
Confidence            777765

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

Probab=82.15  E-value=7.5  Score=39.81  Aligned_cols=55  Identities=25%  Similarity=0.483  Sum_probs=36.6

Q ss_pred             HHHHHHHHH----HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          120 QMMEQLRTE----AQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       120 eYIk~Lq~q----v~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      +.|++|+.+    ++.|+.+...|++++..|..+.+.|+.|+......+..|+.+|..+
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            455566554    4456666677777777777777777777776666677777666654

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=82.01  E-value=6.7  Score=39.10  Aligned_cols=23  Identities=26%  Similarity=0.446  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 026646          142 KIKELKAEKNELRDEKQRLKADK  164 (235)
Q Consensus       142 ei~eLk~EknELr~E~~~Lk~e~  164 (235)
                      +.+.|+.+...++.....|..+.
T Consensus       117 ~~~ql~~~~~~~~~~l~~l~~~l  139 (472)
T TIGR03752       117 EIEQLKSERQQLQGLIDQLQRRL  139 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555555555554433

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.

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

Probab=82.00  E-value=12  Score=30.02  Aligned_cols=68  Identities=22%  Similarity=0.219  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhH-HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 026646           81 CREKLRRDRLNERFLELGSMLEPGRPPKTDKATI-LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDE  156 (235)
Q Consensus        81 ~~ERrRRekINd~F~eLrslLP~~~~~K~dKasI-L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E  156 (235)
                      ...++||..|......+...+-        ..++ +...+.-+..|+.+++.++++++.|..+...|+.+.+.|+++
T Consensus        18 ~~~~~~~~~l~~~l~~~l~~f~--------~~~~~g~~~~~~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg   86 (117)
T COG2919          18 ERRVRRRRILTLVLLALLALFQ--------YLAWFGKNGAADVLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG   86 (117)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHH--------HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            4455566566555555544441        1111 222333334456666666666666666666666666666665

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

Probab=81.75  E-value=7.2  Score=39.95  Aligned_cols=56  Identities=25%  Similarity=0.354  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      .|...|+.+...+++.+.++.+++..|+.|+.........|...+.+|+.|+....
T Consensus        15 ~ya~~lk~e~a~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~eLk~q~~~~~   70 (617)
T PF15070_consen   15 QYAQQLKEESAQWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSELKNQMAEPP   70 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccC
Confidence            49999999999999999999999999999999999999999999999998887543

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

Probab=81.70  E-value=18  Score=30.05  Aligned_cols=64  Identities=17%  Similarity=0.140  Sum_probs=37.3

Q ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          110 DKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       110 dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +...-.+.+++..+.|.+++......+..|+++++........-......|+..+..++.+++.
T Consensus        17 ~~~~~~e~ll~~~~~LE~qL~~~~~~l~lLq~e~~~~e~~le~d~~~L~~Le~~~~~~~~e~~~   80 (160)
T PF13094_consen   17 EDSFDYEQLLDRKRALERQLAANLHQLELLQEEIEKEEAALERDYEYLQELEKNAKALEREREE   80 (160)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445567778888888887776666666666666555444443333444444444444444444

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=81.68  E-value=7.8  Score=35.20  Aligned_cols=33  Identities=15%  Similarity=0.298  Sum_probs=17.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          137 ENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       137 ~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      -+|+.+|+.|+.|+.+||-.+..+.-+++.+++
T Consensus        57 ~~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~   89 (263)
T PRK10803         57 TQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVE   89 (263)
T ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            345555555555555555555555555555443

>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=81.63  E-value=15  Score=25.44  Aligned_cols=29  Identities=38%  Similarity=0.573  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKA  148 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~  148 (235)
                      .|+..|+.++..|+.+|..|..+|..|+.
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            34555555555555555555555555543

; 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 ....

>TIGR02492 flgK_ends flagellar hook-associated protein FlgK

Probab=81.59  E-value=17  Score=33.60  Aligned_cols=78  Identities=18%  Similarity=0.312  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHHhcCC-CCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646           88 DRLNERFLELGSMLE-PGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEK  166 (235)
Q Consensus        88 ekINd~F~eLrslLP-~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~  166 (235)
                      ..||+-|..|.++-- |.  ....+.++|..|-.....++.--..|+........+|+..-.+.|.|-++...|..+|..
T Consensus       107 ~~l~~ff~a~~~ls~~P~--~~~~r~~vl~~a~~l~~~~n~~~~~L~~~~~~~~~~i~~~V~~iN~ll~~Ia~lN~~I~~  184 (322)
T TIGR02492       107 TYLNNFFNALQELAKNPD--SEALRQAVLESAQALANSFNQTSNELQDLRKGINAEIKSAVTEINSLLKQIASLNKEIQQ  184 (322)
T ss_pred             HHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346666666666542 12  456688888888888888887777777766667777777777777777666666666654


Q ss_pred             H
Q 026646          167 L  167 (235)
Q Consensus       167 l  167 (235)
                      .
T Consensus       185 ~  185 (322)
T TIGR02492       185 V  185 (322)
T ss_pred             H
Confidence            3

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

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=81.49  E-value=5.7  Score=37.70  Aligned_cols=44  Identities=20%  Similarity=0.339  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKA  162 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~  162 (235)
                      ..++++|+.+++.|+..+..|..+++.++.+..++++++..|+.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   50 (389)
T PRK03992          7 EERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKS   50 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            45666788899999999999999988888888888777765543

>TIGR00606 rad50 rad50

Probab=81.49  E-value=12  Score=40.99  Aligned_cols=84  Identities=19%  Similarity=0.212  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646           84 KLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKAD  163 (235)
Q Consensus        84 RrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e  163 (235)
                      +..++++++.+..|.+-+...   +..|.. |..++.-..+|+.++.+|..++..+..++++++.+...|..+...+..+
T Consensus       849 ~~e~e~~~~eI~~Lq~ki~el---~~~klk-l~~~l~~r~~le~~L~el~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~  924 (1311)
T TIGR00606       849 RKLIQDQQEQIQHLKSKTNEL---KSEKLQ-IGTNLQRRQQFEEQLVELSTEVQSLIREIKDAKEQDSPLETFLEKDQQE  924 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH---HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            556666777777776666432   223333 3337777778888888888888888887777777777776666666666


Q ss_pred             HHHHHHHH
Q 026646          164 KEKLEQQV  171 (235)
Q Consensus       164 ~e~le~ql  171 (235)
                      .+++..+.
T Consensus       925 ~~~~~~~~  932 (1311)
T TIGR00606       925 KEELISSK  932 (1311)
T ss_pred             HHHHHHHH
Confidence            65544443

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

>TIGR01069 mutS2 MutS2 family protein

Probab=81.47  E-value=9.4  Score=39.94  Aligned_cols=15  Identities=27%  Similarity=0.428  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHh
Q 026646          159 RLKADKEKLEQQVKA  173 (235)
Q Consensus       159 ~Lk~e~e~le~qlk~  173 (235)
                      ..+.+.+.+-.+++.
T Consensus       576 ~a~~~~~~~i~~lk~  590 (771)
T TIGR01069       576 ALKKEVESIIRELKE  590 (771)
T ss_pred             HHHHHHHHHHHHHHh
Confidence            444444444444554

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.

>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=81.38  E-value=9  Score=31.29  Aligned_cols=53  Identities=30%  Similarity=0.429  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          121 MMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       121 YIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      -++.++..++.+..+|..|-+..-.+..+..++|++...+..+...|+.++..
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.

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

Probab=81.28  E-value=16  Score=29.30  Aligned_cols=93  Identities=16%  Similarity=0.260  Sum_probs=65.0

Q ss_pred             chHHHHHHHHHHHHHHHHHHhcCCC---CCCCCCchhhHHH-HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 026646           79 KACREKLRRDRLNERFLELGSMLEP---GRPPKTDKATILS-DAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELR  154 (235)
Q Consensus        79 H~~~ERrRRekINd~F~eLrslLP~---~~~~K~dKasIL~-dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr  154 (235)
                      -.-.+|..|+.   =|..|...|..   ++-...+..-+.. ..+.+++=+|-.++-|-...+.|...+..|+.+...+.
T Consensus        17 ~iDvd~i~~~~---Di~~Lq~~i~~vtf~~l~~e~~~~~~dp~~~klfrLaQl~ieYLl~~q~~L~~~~~~l~~~~~~~~   93 (118)
T PF13815_consen   17 AIDVDRIVREL---DIDTLQENIENVTFCDLENEDCQHFVDPNFLKLFRLAQLSIEYLLHCQEYLSSQLEQLEERLQELQ   93 (118)
T ss_pred             ccCHHHHHhcc---CHHHHHHHHHhcceeccChhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33467777752   24445555543   2111222222222 24577788888899999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhc
Q 026646          155 DEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       155 ~E~~~Lk~e~e~le~qlk~~  174 (235)
                      .+...|+....+...+++.+
T Consensus        94 ~~~~~l~~~~~~~~~~~k~l  113 (118)
T PF13815_consen   94 QEIEKLKQKLKKQKEEIKKL  113 (118)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999998865

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

Probab=81.15  E-value=16  Score=28.68  Aligned_cols=27  Identities=30%  Similarity=0.551  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          139 LQEKIKELKAEKNELRDEKQRLKADKE  165 (235)
Q Consensus       139 L~~ei~eLk~EknELr~E~~~Lk~e~e  165 (235)
                      ++.++++|..+++.|.+|+..|+.+++
T Consensus        47 wek~v~~L~~e~~~l~~E~e~L~~~l~   73 (87)
T PF12709_consen   47 WEKKVDELENENKALKRENEQLKKKLD   73 (87)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444433

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 [].

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

Probab=81.14  E-value=8.9  Score=34.18  Aligned_cols=76  Identities=24%  Similarity=0.284  Sum_probs=39.8

Q ss_pred             HHHhcCCCCCCCCCchhhHH-----------HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH-------HHHHHH
Q 026646           96 ELGSMLEPGRPPKTDKATIL-----------SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKN-------ELRDEK  157 (235)
Q Consensus        96 eLrslLP~~~~~K~dKasIL-----------~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~Ekn-------ELr~E~  157 (235)
                      .|.+||..+- -..+|..+-           .+---|...|+.+.+.+.+....|.+.+...++-..       +|..+.
T Consensus        47 vLQsLvDD~l-V~~eKIgtSnyywsfps~a~~~~ks~~qeLe~~L~~~~qk~~tl~e~~en~K~~~e~tEer~~el~kkl  125 (203)
T KOG3433|consen   47 VLQSLVDDGL-VIKEKIGTSNYYWSFPSEAICDRKSVLQELESQLATGSQKKATLGESIENRKAGREETEERTDELTKKL  125 (203)
T ss_pred             HHHHHhccch-HHHHHhcccccccccchHHHHHHHHHHHHHHHHHHHhhhhHhHHHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence            5666676542 234444443           233346667777777777766666666555444332       333344


Q ss_pred             HHHHHHHHHHHHHHH
Q 026646          158 QRLKADKEKLEQQVK  172 (235)
Q Consensus       158 ~~Lk~e~e~le~qlk  172 (235)
                      ..|+.+++.+..+|.
T Consensus       126 nslkk~~e~lr~el~  140 (203)
T KOG3433|consen  126 NSLKKILESLRWELA  140 (203)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            444444444444444

>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=81.06  E-value=8.9  Score=32.44  Aligned_cols=8  Identities=50%  Similarity=0.621  Sum_probs=2.8

Q ss_pred             HHHHHHHH
Q 026646          146 LKAEKNEL  153 (235)
Q Consensus       146 Lk~EknEL  153 (235)
                      |+.++.+|
T Consensus        56 Lk~~i~~l   63 (155)
T PF06810_consen   56 LKKQIEEL   63 (155)
T ss_pred             HHHHHHHH
Confidence            33333333

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

>PRK04325 hypothetical protein; Provisional

Probab=81.02  E-value=8.6  Score=28.82  Aligned_cols=49  Identities=8%  Similarity=0.094  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      +.|.+|+.++.-++...+.|...+-.-..++..|+.+...|...+..++
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            4577888888888888888877777777777777777777765555443

>COG5570 Uncharacterized small protein [Function unknown]

Probab=81.01  E-value=5.5  Score=28.84  Aligned_cols=21  Identities=48%  Similarity=0.591  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 026646          150 KNELRDEKQRLKADKEKLEQQ  170 (235)
Q Consensus       150 knELr~E~~~Lk~e~e~le~q  170 (235)
                      +-+|...|-+||.+||+|..|
T Consensus        35 i~eLKRrKL~lKeeIEkLka~   55 (57)
T COG5570          35 IRELKRRKLRLKEEIEKLKAQ   55 (57)
T ss_pred             HHHHHHHHHHHHHHHHHHhcc
Confidence            345556667777777777655

>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=80.58  E-value=11  Score=32.84  Aligned_cols=18  Identities=22%  Similarity=0.268  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHHHHHhcCC
Q 026646           85 LRRDRLNERFLELGSMLE  102 (235)
Q Consensus        85 rRRekINd~F~eLrslLP  102 (235)
                      .|++=.|..|.+|---|-
T Consensus        59 vr~~ly~~~F~ELIRQVT   76 (189)
T PF10211_consen   59 VREELYSQCFDELIRQVT   76 (189)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            355666667777665553

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 [].

>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []

Probab=80.53  E-value=11  Score=36.16  Aligned_cols=78  Identities=24%  Similarity=0.320  Sum_probs=47.7

Q ss_pred             HHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Q 026646           92 ERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKE---LKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus        92 d~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~e---Lk~EknELr~E~~~Lk~e~e~le  168 (235)
                      +-|..|-...+..  .+.==|.|  +--+|++.|++++++|+.+.++|.+++++   .+..+.++.++..++..+++.++
T Consensus       218 ~Yf~~l~~~f~d~--a~~~~A~l--~~~~~~~~l~~~~~~~~~~i~~l~~~l~~~~k~~~k~~~~~~q~~~~~k~~~~~~  293 (406)
T PF02388_consen  218 EYFENLYDAFGDK--AKFFLAEL--NGKEYLESLQEKLEKLEKEIEKLEEKLEKNPKKKNKLKELEEQLASLEKRIEEAE  293 (406)
T ss_dssp             HHHHHHHHHCCCC--EEEEEEEE--CCHHHHHHHHHHHHHHHHHHHHHHHHHHH-THHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCC--eEEEEEEE--cHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHHHHHHH
Confidence            4577777777432  11111111  12367777777777777777777665443   33445567777778888888887


Q ss_pred             HHHHh
Q 026646          169 QQVKA  173 (235)
Q Consensus       169 ~qlk~  173 (235)
                      ..+..
T Consensus       294 ~~~~~  298 (406)
T PF02388_consen  294 ELIAE  298 (406)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            77665

These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.

>PRK04654 sec-independent translocase; Provisional

Probab=80.47  E-value=15  Score=33.25  Aligned_cols=49  Identities=16%  Similarity=0.146  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          117 DAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEK  166 (235)
Q Consensus       117 dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~  166 (235)
                      ..-++|+++|+.....+++..+ +.++++|+.+.++++.+...++.++..
T Consensus        31 tlGk~irk~R~~~~~vk~El~~-El~~~ELrk~l~~~~~~i~~~~~~lk~   79 (214)
T PRK04654         31 FAGLWVRRARMQWDSVKQELER-ELEAEELKRSLQDVQASLREAEDQLRN   79 (214)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-hhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445666666665555554322 112334444444433333333333333

>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=80.45  E-value=22  Score=26.69  Aligned_cols=32  Identities=22%  Similarity=0.506  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNEL  153 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknEL  153 (235)
                      +++|++.++++.+....+++++..+..|.+++
T Consensus        21 l~~l~~~l~~~~~ti~~l~~~~~~i~~e~~~l   52 (90)
T PF06103_consen   21 LKKLKKTLDEVNKTIDTLQEQVDPITKEINDL   52 (90)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            33444444444444444444444444444443

>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=80.41  E-value=17  Score=32.89  Aligned_cols=19  Identities=26%  Similarity=0.433  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 026646          152 ELRDEKQRLKADKEKLEQQ  170 (235)
Q Consensus       152 ELr~E~~~Lk~e~e~le~q  170 (235)
                      .+.+|...||.+++++..+
T Consensus        85 r~~eey~~Lk~~in~~R~e  103 (230)
T PF10146_consen   85 RLYEEYKPLKDEINELRKE  103 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444

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.

>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]

Probab=80.32  E-value=2.2  Score=43.27  Aligned_cols=40  Identities=20%  Similarity=0.389  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026646          137 ENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA  176 (235)
Q Consensus       137 ~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~  176 (235)
                      ..|+..+++|.+|...||.||..||.+++-+..+=+.+-+
T Consensus       305 ~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~En~~~kv  344 (655)
T KOG4343|consen  305 LGLEARLQALLSENEQLKKENATLKRQLDELVSENQRLKV  344 (655)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCccccc
Confidence            3455555666666556666666666666655554443333

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

Probab=80.22  E-value=22  Score=26.56  Aligned_cols=54  Identities=31%  Similarity=0.479  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      .+--..|..+...+...+.+|+.++.++..+..+|......+..+++.|+..++
T Consensus        18 ~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l~~~l~   71 (74)
T PF12329_consen   18 MEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESLEERLK   71 (74)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            333445555555566666666666666666666666666666666666666654

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.

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

Probab=80.14  E-value=20  Score=36.50  Aligned_cols=85  Identities=24%  Similarity=0.421  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCchhhH-HHHHHHHHHHHHHHHHHHHH---HhHHHHHHHHHHHHHHHHHHHHHHH
Q 026646           84 KLRRDRLNERFLELGSMLEPGRPPKTDKATI-LSDAVQMMEQLRTEAQKLKQ---SNENLQEKIKELKAEKNELRDEKQR  159 (235)
Q Consensus        84 RrRRekINd~F~eLrslLP~~~~~K~dKasI-L~dAIeYIk~Lq~qv~~L~~---e~~~L~~ei~eLk~EknELr~E~~~  159 (235)
                      =.|=+++.+|+..|+.+-        .|-.. +.+.++|..+++.+.+.|..   ..++|+.+++.++.+..+.-...+.
T Consensus       296 p~~L~~ve~Rl~~L~~l~--------RKY~~~~~~l~~~~~~~~~el~~L~~~~~~~~~Le~~~~~l~~~~~~~A~~Ls~  367 (557)
T COG0497         296 PNRLEEVEERLFALKSLA--------RKYGVTIEDLLEYLDKIKEELAQLDNSEESLEALEKEVKKLKAELLEAAEALSA  367 (557)
T ss_pred             HHHHHHHHHHHHHHHHHH--------HHhCCCHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346678888888888875        34444 88999999999999998886   3567777888888777776666654


Q ss_pred             HHHHH-----HHHHHHHHhccC
Q 026646          160 LKADK-----EKLEQQVKAMSA  176 (235)
Q Consensus       160 Lk~e~-----e~le~qlk~~~~  176 (235)
                      .+...     ..+.++|+.++.
T Consensus       368 ~R~~~A~~L~~~v~~eL~~L~M  389 (557)
T COG0497         368 IRKKAAKELEKEVTAELKALAM  389 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCC
Confidence            44332     345666777655

>PRK04406 hypothetical protein; Provisional

Probab=80.12  E-value=12  Score=28.28  Aligned_cols=49  Identities=10%  Similarity=0.200  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKL  167 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~l  167 (235)
                      -+.|.+|+.++.-++...+.|...+-....++..|+.+...|...+..+
T Consensus        10 e~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~~   58 (75)
T PRK04406         10 EERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVKNM   58 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3477788888888888888887777777777777777777775555443

---

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	235
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	8e-14
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	1e-13
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	3e-13
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	2e-10
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	1e-08
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	1e-08
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	7e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	8e-04
4f3l_A	361	Mclock, circadian locomoter output cycles protein	2e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-04
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	2e-04
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-04
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	4e-04
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	5e-04
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	6e-04

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

 Score = 63.9 bits (156), Expect = 8e-14
 Identities = 16/72 (22%), Positives = 34/72 (47%)

Query: 83  EKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEK 142
           E+ RRD + + F  L   +   +  K  +A IL  A + ++ +R +    +Q  ++L+ +
Sbjct: 10  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ 69

Query: 143 IKELKAEKNELR 154
              L+ +   L 
Sbjct: 70  NALLEQQVRALG 81

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

 Score = 63.1 bits (154), Expect = 1e-13
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 83  EKLRRDRLNERFLELGSML-EPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQE 141
           E+ RR+ L   F  L   + E     K  K  IL  A   +  ++ E QKL    + L++
Sbjct: 14  ERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK 73

Query: 142 KIKELKAEKNELR 154
           + ++LK +  +L 
Sbjct: 74  RREQLKHKLEQLG 86

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

 Score = 62.4 bits (152), Expect = 3e-13
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 83  EKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEK 142
           EK  R  +N++ +EL  ++  G   K +K+ +L  A+  +  L+   QKLKQ N +L+  
Sbjct: 14  EKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA 72

Query: 143 IKELKAEK 150
           + + 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 = 54.3 bits (131), Expect = 2e-10
 Identities = 14/60 (23%), Positives = 30/60 (50%)

Query: 83  EKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEK 142
           E+ RRD + + F  L   +   +  K  +A IL  A + ++ +R +    +Q  ++L+ +
Sbjct: 20  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ 79

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1 Length = 65

 Score = 49.3 bits (118), Expect = 1e-08
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 83  EKLRRDRLNERFLELGSML----EPGRPPKTDKATILSDAVQMMEQLRTEAQK 131
           E+ RRD++N   ++L  ++             K  ILS A   +++LR    +
Sbjct: 13  ERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR 65

>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 = 49.4 bits (118), Expect = 1e-08
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 83  EKLRRDRLNERFLELGSML-EPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQE 141
           EK RR  L     +L  ++       +    ++L+ A   +++L    +K     + LQ 
Sbjct: 9   EKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR 68

Query: 142 KIKELKAEKNEL 153
           + + LK +  +L
Sbjct: 69  EQRHLKRQLEKL 80

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 387

 Score = 48.5 bits (115), Expect = 7e-07
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 64  SRKRLRSESCCVSGSKACREKLRRDRLNERFLELGSML--EPGRPPKTDKATILSDAVQM 121
           +  + R ++   + S+   EK RRD++N    EL S++        K DK T+L  AVQ 
Sbjct: 4   AEHQGRIKNAREAHSQI--EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQH 61

Query: 122 MEQLRTEAQKLKQSNEN 138
           M+ LR       ++N  
Sbjct: 62  MKTLRGATNPYTEANYK 78

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.7 bits (116), Expect = 7e-07
 Identities = 17/99 (17%), Positives = 45/99 (45%), Gaps = 2/99 (2%)

Query: 79   KACREKLRR--DRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSN 136
            +  R++L +   +L     +L   +   +    +    L+   + ++      +      
Sbjct: 1052 EKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQK 1111

Query: 137  ENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS 175
             N  +KI+EL++  ++L+++ +  KA + K E+Q + +S
Sbjct: 1112 NNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDLS 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 = 47.1 bits (112), Expect = 2e-06
 Identities = 19/119 (15%), Positives = 46/119 (38%), Gaps = 2/119 (1%)

Query: 58   KEVEAGSRKRLRSESCCVSGSKACREKL--RRDRLNERFLELGSMLEPGRPPKTDKATIL 115
            +E+      R+  E       +A ++K+  +   L E+  E  +  +  +  K      +
Sbjct: 926  EEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKI 985

Query: 116  SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 174
                  +  +  +  KL +  + L+E++ +L     E  ++ + L   K K E  +  +
Sbjct: 986  KKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISEL 1044

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 45.2 bits (107), Expect = 1e-05
 Identities = 20/120 (16%), Positives = 50/120 (41%), Gaps = 1/120 (0%)

Query: 58   KEVEAGSRKRLRSESCCVSGSKACREKLRR-DRLNERFLELGSMLEPGRPPKTDKATILS 116
            ++++A +     +E   V  +   +E       +  R  E     +  +  K      + 
Sbjct: 899  EKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQML 958

Query: 117  DAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA 176
            D  + +E+     QKL+        KIK+++ +   + D+  +L  +++ LE++V  ++ 
Sbjct: 959  DLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTT 1018

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 43.7 bits (103), Expect = 3e-05
 Identities = 19/110 (17%), Positives = 49/110 (44%), Gaps = 19/110 (17%)

Query: 65  RKRLRSESCCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQ 124
           +++L++E+           +  R RL  +  EL  +L               +    +E+
Sbjct: 898 QEKLQAET-----ELYAEAEEMRVRLAAKKQELEEILH--------------EMEARIEE 938

Query: 125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 174
               +Q+L+   + +Q+++ +L+ +  E    +Q+L+ +K   + ++K M
Sbjct: 939 EEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKM 988

>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 = 6e-05
 Identities = 10/58 (17%), Positives = 24/58 (41%)

Query: 115  LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 172
            +SD  + +E  +    K ++   +L E+++ LK E  +  D     +  +    +   
Sbjct: 1125 ISDLQEDLESEKAARNKAEKQKRDLSEELEALKTELEDTLDTTATQQELRGSDYKDDD 1182

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 39.4 bits (92), Expect = 8e-04
 Identities = 12/58 (20%), Positives = 31/58 (53%)

Query: 115  LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 172
            L    +  ++L    +KL+  + +L E+I EL+A+  EL+ +  + + + +    +++
Sbjct: 1048 LKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLE 1105

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 361

 Score = 46.9 bits (111), Expect = 2e-06
 Identities = 29/99 (29%), Positives = 45/99 (45%), Gaps = 9/99 (9%)

Query: 63  GSRKRLRSESC-CVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQM 121
           G+ +    +    VS +K+  EK RRD+ N    ELGSML PG   K DK+T+L  ++  
Sbjct: 1   GAVEEDDKDKAKRVSRNKS--EKKRRDQFNVLIKELGSML-PGNARKMDKSTVLQKSID- 56

Query: 122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRL 160
              LR    K   +  +  E  ++ K       +  Q +
Sbjct: 57  --FLRK--HKETTAQSDASEIRQDWKPTFLSNEEFTQLM 91

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

 Score = 43.6 bits (103), Expect = 3e-05
 Identities = 13/57 (22%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 123 EQLRTEA---QKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA 176
           ++L+ EA   ++ K+ +  L+ KI +L+ + +E   E + L      LE      + 
Sbjct: 907 KKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETE 963

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

 Score = 43.6 bits (103), Expect = 3e-05
 Identities = 13/58 (22%), Positives = 31/58 (53%), Gaps = 4/58 (6%)

Query: 122  MEQLRTEAQKLKQSNENLQEKIKELKAE----KNELRDEKQRLKADKEKLEQQVKAMS 175
            + +LR E  + +   + ++E   + K E     +EL+++   LK +KE+L +++   +
Sbjct: 993  IAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQA 1050

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

 Score = 40.1 bits (94), Expect = 4e-04
 Identities = 6/62 (9%), Positives = 22/62 (35%)

Query: 115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 174
           + +  +  + L  +   L+ +     EK++          +E +        L++++  +
Sbjct: 937 IDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKL 996

Query: 175 SA 176
             
Sbjct: 997 RK 998

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A Length = 62

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 13/44 (29%), Positives = 24/44 (54%)

Query: 130 QKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 173
           ++  +    L+EK+K LKA+ +EL      L+    +L+Q+V  
Sbjct: 18  KRKLERIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKVMN 61

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

 Score = 39.4 bits (91), Expect = 3e-04
 Identities = 9/51 (17%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ 169
           +   ++L  E + +++  E  +++++E     +++ +++ R KA K+  E 
Sbjct: 74  IAQADRLTQEPESIRKWREEQRKRLQE-LDAASKVMEQEWREKAKKDLEEW 123

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 418

 Score = 39.8 bits (92), Expect = 4e-04
 Identities = 15/56 (26%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS 175
               +L+   ++ +Q  +NL+ + KEL+ ++ +  DEK   +A +  LEQQ  + +
Sbjct: 355 DSEAELQ---RRHEQMKKNLEAQHKELEEKRRQFEDEKANWEAQQRILEQQNSSRT 407

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1 Length = 61

 Score = 36.6 bits (85), Expect = 5e-04
 Identities = 12/44 (27%), Positives = 26/44 (59%)

Query: 130 QKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 173
           QK K   ++L++K ++L +   +L+ E   L+ +  +L+Q + A
Sbjct: 18  QKRKVWVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLKQLLLA 61

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A* Length = 76

 Score = 36.8 bits (85), Expect = 6e-04
 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 5/59 (8%)

Query: 82  REKLRRDRLNERFLELGSMLEPGRPP--KTDKATILSDAVQMMEQLRTEAQKLKQSNEN 138
            E+ RR  +NE F ELG M +          K  IL  AVQ++  L    Q++++ N N
Sbjct: 12  LERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLE---QQVRERNLN 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	235
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.76
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.76
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.73
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.71
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.69
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.68
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.59
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.58
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.52
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.48
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.47
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.3
4ath_A	83	MITF, microphthalmia-associated transcription fact	99.22
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.19
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.07
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.91
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.72
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	97.97
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	97.54
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	96.58
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	96.45
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	96.08
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	96.02
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	95.44
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	95.42
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	95.14
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	95.04
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	95.02
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	94.95
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	94.69
2oqq_A	42	Transcription factor HY5; homodimer leucine zipper	94.47
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	94.47
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	94.3
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	93.63
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	93.56
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	93.25
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	93.07
1deb_A	54	APC protein, adenomatous polyposis coli protein; c	93.06
3cve_A	72	Homer protein homolog 1; coiled coil, alternative	92.98
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	92.66
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	92.54
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	92.52
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	92.33
2wt7_B	90	Transcription factor MAFB; transcription, transcri	92.21
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	92.17
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	92.09
3he5_B	52	Synzip2; heterodimeric coiled-coil, de novo protei	92.0
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	91.75
3htk_A	60	Structural maintenance of chromosomes protein 5; S	91.68
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	91.5
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	91.36
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	90.97
3cvf_A	79	Homer-3, homer protein homolog 3; coiled coil, alt	90.53
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	90.4
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	90.21
3swf_A	74	CGMP-gated cation channel alpha-1; coiled-coil, as	90.21
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	90.03
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	90.01
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	89.94
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	89.87
3swy_A	46	Cyclic nucleotide-gated cation channel alpha-3; co	89.8
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	89.72
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	89.64
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	89.45
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	88.95
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	88.82
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	88.8
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	88.75
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	88.69
3he5_A	49	Synzip1; heterodimeric coiled-coil, de novo protei	88.59
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	88.33
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	88.25
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	87.79
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	87.79
3htk_A	60	Structural maintenance of chromosomes protein 5; S	87.76
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	87.64
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	87.57
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	87.56
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	86.96
3m48_A	33	General control protein GCN4; leucine zipper, synt	86.91
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	86.68
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	86.61
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	86.57
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	86.49
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	86.28
2oxj_A	34	Hybrid alpha/beta peptide based on the GCN4-P1 Se	86.22
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	86.19
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	86.15
2w6a_A	63	ARF GTPase-activating protein GIT1; PIX, zinc, sig	86.09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	86.04
1kd8_A	36	GABH AIV, GCN4 acid base heterodimer acid-D12IA16V	85.9
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	85.76
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	85.7
1gk6_A	59	Vimentin; intermediate filament, dimer, parallel c	85.7
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	85.7
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	85.67
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	85.49
3c3g_A	33	Alpha/beta peptide with the GCN4-PLI SIDE chain S	85.3
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	85.24
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	85.19
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	85.01
3vmx_A	48	Voltage-gated hydrogen channel 1; coiled-coil, ION	84.95
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	84.81
2wq1_A	33	General control protein GCN4; TAA, nucleus, coiled	84.38
2wt7_B	90	Transcription factor MAFB; transcription, transcri	84.35
1m1j_C	409	Fibrinogen gamma chain; coiled coils, disulfide ri	84.18
1kd8_B	36	GABH BLL, GCN4 acid base heterodimer base-D12LA16L	84.1
3u06_A	412	Protein claret segregational; motor domain, stalk	83.99
3c3f_A	34	Alpha/beta peptide with the GCN4-PLI SIDE chain S	83.98
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	83.96
3v86_A	27	De novo design helix; computational design of A pr	83.93
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	83.87
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	83.59
3iv1_A	78	Tumor susceptibility gene 101 protein; coiled_COIL	83.58
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	83.1
2zvf_A	171	Alanyl-tRNA synthetase; C-terminal, oligomerizatio	83.06
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	82.85
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	82.82
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	82.63
1gmj_A	84	ATPase inhibitor; coiled-coil structure, P depende	82.6
1wt6_A	81	Myotonin-protein kinase; coiled-coil, kinase activ	82.58
3swk_A	86	Vimentin; cytoskeleton, intermediate filament, alp	82.55
3a7o_A	75	Autophagy protein 16; coiled-coil, coiled coil, cy	82.36
1uix_A	71	RHO-associated kinase; coiled-coil, transferase; H	82.21
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	82.14
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	82.08
1x8y_A	86	Lamin A/C; structural protein, intermediate filame	82.03
1kd8_B	36	GABH BLL, GCN4 acid base heterodimer base-D12LA16L	81.57
1uo4_A	34	General control protein GCN4; four helix bundle, c	81.56
2bni_A	34	General control protein GCN4; four helix bundle, a	81.33
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	81.03
3m48_A	33	General control protein GCN4; leucine zipper, synt	80.64
3vmx_A	48	Voltage-gated hydrogen channel 1; coiled-coil, ION	80.5
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	80.47
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	80.23
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	80.23
1kd8_A	36	GABH AIV, GCN4 acid base heterodimer acid-D12IA16V	80.21
4dzn_A	33	Coiled-coil peptide CC-PIL; de novo protein; HET:	80.07

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

Probab=99.76  E-value=1.3e-18  Score=130.97  Aligned_cols=72  Identities=26%  Similarity=0.389  Sum_probs=66.1

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELK  147 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk  147 (235)
                      ++.+|+.+||+||++||++|.+|+++||.+ ..|+||++||.+||+||++|+.+++.|+.+++.|+..+++.+
T Consensus         6 rr~~H~~~ErrRR~~in~~f~~L~~lvP~~-~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~~~~~   77 (82)
T 1am9_A            6 KRTAHNAIEKRYRSSINDKIIELKDLVVGT-EAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTCS-SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHhccCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            467899999999999999999999999975 379999999999999999999999999999999988876653

>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=99.76  E-value=1.7e-18  Score=129.84  Aligned_cols=75  Identities=20%  Similarity=0.328  Sum_probs=64.1

Q ss_pred             cCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 026646           76 SGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEK  150 (235)
Q Consensus        76 ~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~Ek  150 (235)
                      +.+|+.+||+||++||+.|.+|+++||.....|++|++||.+||+||+.|+.+++.|+.+.+.|..++..|+.+.
T Consensus         3 R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~~~~L~~~l   77 (83)
T 1nkp_B            3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQV   77 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            568999999999999999999999999865589999999999999999999999998777666655555554443

>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=99.73  E-value=4.7e-18  Score=129.82  Aligned_cols=80  Identities=24%  Similarity=0.337  Sum_probs=69.3

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGR-PPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNEL  153 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~-~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknEL  153 (235)
                      .+.+|+.+||+||++||++|..|+++||... ..|.+|++||.+||+||++|+.+.+.|..+.+.|+.+...|+.+..+|
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            5678999999999999999999999999752 369999999999999999999999999888887777777776666555


Q ss_pred             H
Q 026646          154 R  154 (235)
Q Consensus       154 r  154 (235)
                      +
T Consensus        86 ~   86 (88)
T 1nkp_A           86 G   86 (88)
T ss_dssp             C
T ss_pred             h
Confidence            3

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

Probab=99.71  E-value=3.1e-17  Score=123.40  Aligned_cols=76  Identities=20%  Similarity=0.282  Sum_probs=67.5

Q ss_pred             cCcchHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 026646           76 SGSKACREKLRRDRLNERFLELGSMLEPG-RPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKN  151 (235)
Q Consensus        76 ~~sH~~~ERrRRekINd~F~eLrslLP~~-~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~Ekn  151 (235)
                      +.+|+..||+||++||++|..|+++||.. ...|.+|++||.+|++||++|+.+.++|..+++.|+.++.+|+.+.+
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~e~~~L~~~L~   78 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLE   78 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45799999999999999999999999965 33799999999999999999999999999998888888777766554

>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=3.1e-17  Score=131.30  Aligned_cols=87  Identities=25%  Similarity=0.386  Sum_probs=53.5

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCC--CCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRP--PKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNE  152 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~--~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknE  152 (235)
                      .+.+|+..||+||++||++|.+|+++||.+..  .|++|++||.+||+||++|+++++.|+++...+.           .
T Consensus        27 kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~~~~-----------~   95 (118)
T 4ati_A           27 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQK-----------K   95 (118)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC---------------
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------H
Confidence            46789999999999999999999999998742  5899999999999999999999999987643321           2


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 026646          153 LRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       153 Lr~E~~~Lk~e~e~le~qlk  172 (235)
                      |+.++..|...+..||.|..
T Consensus        96 l~~~n~~L~~riqeLE~~a~  115 (118)
T 4ati_A           96 LEHANRHLLLRVQELEMQAR  115 (118)
T ss_dssp             --------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            33344444455555555443

>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=99.68  E-value=6.1e-17  Score=120.88  Aligned_cols=68  Identities=21%  Similarity=0.358  Sum_probs=62.7

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEK  142 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~e  142 (235)
                      .+.+|+.+||+||++||+.|.+|+++||.....|++|++||..||+||+.|+++++.|+.+++.|+.+
T Consensus        12 ~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~~   79 (80)
T 1hlo_A           12 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ   79 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            57789999999999999999999999998755799999999999999999999999999998888653

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.59  E-value=1.2e-15  Score=113.02  Aligned_cols=58  Identities=33%  Similarity=0.421  Sum_probs=52.1

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLK  133 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~  133 (235)
                      .+.+|+..||+||++||++|.+|+++||.+ ..|+||++||.+||+||++|+.++.=|+
T Consensus         8 kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~-~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            8 KRVSRNKSEKKRRDQFNVLIKELGSMLPGN-ARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSSSC-CSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HhhhhhHHHhhHHHHHHHHHHHHHHhCCCC-CCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            467899999999999999999999999964 3799999999999999999999876543

>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=99.58  E-value=4.4e-16  Score=111.81  Aligned_cols=56  Identities=23%  Similarity=0.373  Sum_probs=50.6

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCC----CCCchhhHHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRP----PKTDKATILSDAVQMMEQLRTEAQ  130 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~----~K~dKasIL~dAIeYIk~Lq~qv~  130 (235)
                      .+.+|+..||+||++||+.|.+|+++||.+..    .|++|++||.+||+||++|+++++
T Consensus         5 rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A            5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            56789999999999999999999999998754    389999999999999999998653

>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=99.52  E-value=1.5e-15  Score=109.52  Aligned_cols=55  Identities=25%  Similarity=0.349  Sum_probs=49.1

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCC-----CCCCchhhHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGR-----PPKTDKATILSDAVQMMEQLRTEA  129 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~-----~~K~dKasIL~dAIeYIk~Lq~qv  129 (235)
                      .+.+|+.+||+||++||++|.+|++|||.+.     ..|.+||+||+.||+||++|++++
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            3678999999999999999999999999641     268889999999999999999765

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A*

Probab=99.48  E-value=1.4e-14  Score=108.27  Aligned_cols=60  Identities=30%  Similarity=0.364  Sum_probs=49.6

Q ss_pred             cCcCcchHHHHHHHHHHHHHHHHHHhcCCC-CCCCCC-chhhHHHHHHHHHHHHHHHHHHHH
Q 026646           74 CVSGSKACREKLRRDRLNERFLELGSMLEP-GRPPKT-DKATILSDAVQMMEQLRTEAQKLK  133 (235)
Q Consensus        74 ~~~~sH~~~ERrRRekINd~F~eLrslLP~-~~~~K~-dKasIL~dAIeYIk~Lq~qv~~L~  133 (235)
                      .++.+|+.+||+||++||++|.+|+.+||. ....|. +|++||..||+||+.|++++++++
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            467789999999999999999999999994 333566 799999999999999999998765

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.47  E-value=9.3e-15  Score=108.46  Aligned_cols=53  Identities=38%  Similarity=0.421  Sum_probs=47.9

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCchhhHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGR--PPKTDKATILSDAVQMMEQLRT  127 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~--~~K~dKasIL~dAIeYIk~Lq~  127 (235)
                      ++.+|+..||+||++||+.|.+|++|||.+.  ..|+||++||..||+||+.|+.
T Consensus         9 rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            4667999999999999999999999999652  2699999999999999999974

>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=99.30  E-value=1e-12  Score=96.25  Aligned_cols=56  Identities=23%  Similarity=0.287  Sum_probs=50.8

Q ss_pred             cCcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHH
Q 026646           74 CVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEA  129 (235)
Q Consensus        74 ~~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv  129 (235)
                      ..+..|+.+||+|+..||+.|..|+++||.....|.+|+.||..||+||..|++.+
T Consensus        11 ~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           11 DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            46778999999999999999999999999654479999999999999999999754

>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus}

Probab=99.22  E-value=1.1e-10  Score=88.77  Aligned_cols=52  Identities=29%  Similarity=0.470  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHhcCCCCC--CCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHH
Q 026646           87 RDRLNERFLELGSMLEPGR--PPKTDKATILSDAVQMMEQLRTEAQKLKQSNEN  138 (235)
Q Consensus        87 RekINd~F~eLrslLP~~~--~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~  138 (235)
                      |..||++|.+|+.+||++.  ..|.+|++||..||+||+.||++++++.++...
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r   57 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENR   57 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8899999999999999753  379999999999999999999998888776543

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}

Probab=99.19  E-value=1.7e-11  Score=87.58  Aligned_cols=55  Identities=20%  Similarity=0.076  Sum_probs=49.0

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCchhhHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGR-PPKTDKATILSDAVQMMEQLRTEA  129 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~-~~K~dKasIL~dAIeYIk~Lq~qv  129 (235)
                      ++..|+.+||+|+..||+.|..|+.+||... ..|.+|+.||..||+||..|++.+
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            3556899999999999999999999999642 379999999999999999999765

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.07  E-value=1.2e-10  Score=105.45  Aligned_cols=53  Identities=34%  Similarity=0.463  Sum_probs=42.4

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTE  128 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~q  128 (235)
                      .+.+|+..||+||++||..|.+|++|||. ...|+||++||..||.||+.|+..
T Consensus        12 ~~~~~~~~e~~rr~~~n~~~~~l~~~~p~-~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           12 KRVSRNKSEKKRRDQFNVLIKELGSMLPG-NARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHTCCS-SSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHhCCC-CCCCcCHHHHHHHHHHHHHHHHhh
Confidence            35569999999999999999999999993 347999999999999999998764

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=98.91  E-value=6.1e-10  Score=102.09  Aligned_cols=54  Identities=37%  Similarity=0.401  Sum_probs=47.7

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCC--CCCCCchhhHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPG--RPPKTDKATILSDAVQMMEQLRTE  128 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~--~~~K~dKasIL~dAIeYIk~Lq~q  128 (235)
                      .+.+|+..||+||++||+.|.+|+++||.+  ...|+||++||..||+||+.|+..
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            366799999999999999999999999942  127999999999999999999854

>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=98.72  E-value=3e-09  Score=78.17  Aligned_cols=49  Identities=14%  Similarity=0.158  Sum_probs=43.6

Q ss_pred             chHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCchhhHHHHHHHHHHHHHH
Q 026646           79 KACREKLRRDRLNERFLELGSMLEPGR-PPKTDKATILSDAVQMMEQLRT  127 (235)
Q Consensus        79 H~~~ERrRRekINd~F~eLrslLP~~~-~~K~dKasIL~dAIeYIk~Lq~  127 (235)
                      -+.+||+|+..||+.|..|+.+||... ..|.+|+.||..||+||..||.
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            347999999999999999999999642 2699999999999999999984

>4aya_A DNA-binding protein inhibitor ID-2; cell cycle; 2.10A {Homo sapiens}

Probab=97.97  E-value=1.6e-05  Score=61.87  Aligned_cols=52  Identities=13%  Similarity=0.128  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCC-CCCCchhhHHHHHHHHHHHHHHHHHHH
Q 026646           81 CREKLRRDRLNERFLELGSMLEPGR-PPKTDKATILSDAVQMMEQLRTEAQKL  132 (235)
Q Consensus        81 ~~ERrRRekINd~F~eLrslLP~~~-~~K~dKasIL~dAIeYIk~Lq~qv~~L  132 (235)
                      ..||.|=..||+.|..|+.+||... ..|.+|..||.-||+||..|+..++.-
T Consensus        31 ~~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~   83 (97)
T 4aya_A           31 DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSH   83 (97)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             ccHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhcC
Confidence            3457788899999999999999642 279999999999999999999877653

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=97.54  E-value=0.00069  Score=51.16  Aligned_cols=59  Identities=22%  Similarity=0.480  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +..||+-|.-||-++++|+.+|..|.++.++++.....|+.|+..|+.|....+..|.+
T Consensus        15 Iq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~~   73 (81)
T 2jee_A           15 VQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQA   73 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56788999999999999999999999999998888888888999898888877777665

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=96.58  E-value=0.014  Score=43.94  Aligned_cols=56  Identities=29%  Similarity=0.424  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhc
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQR-------LKADKEKLEQQVKAM  174 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~-------Lk~e~e~le~qlk~~  174 (235)
                      .+.+.+|..+|+.+-..+.-|+.+|++||.+.+.|.+++..       |..++++|+++..++
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            46788899999988888888888888888877777777776       666777777776654

>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=96.45  E-value=0.022  Score=40.25  Aligned_cols=57  Identities=26%  Similarity=0.391  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 026646           83 EKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELR  154 (235)
Q Consensus        83 ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr  154 (235)
                      ||++|-+..++..+.++     +          ..-.+|+..|+.++..|+.+|..|..+|..|+.++..|+
T Consensus         1 Ekr~rrrerNR~AA~rc-----R----------~rKk~~~~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk   57 (63)
T 2wt7_A            1 EKRRIRRERNKMAAAKC-----R----------NRRRELTDTLQAETDQLEDEKSALQTEIANLLKEKEKLE   57 (63)
T ss_dssp             CHHHHHHHHHHHHHHHH-----H----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHhHHHHHHH-----H----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45555555555555554     1          344578888888888888888888877766666555554

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

Probab=96.08  E-value=0.057  Score=43.84  Aligned_cols=81  Identities=21%  Similarity=0.214  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHhc--CCCCCCCCCchhhHHHH---HHHHHHHHHHHHHHHHHHhHHH--------------HHHHHHHHH
Q 026646           88 DRLNERFLELGSM--LEPGRPPKTDKATILSD---AVQMMEQLRTEAQKLKQSNENL--------------QEKIKELKA  148 (235)
Q Consensus        88 ekINd~F~eLrsl--LP~~~~~K~dKasIL~d---AIeYIk~Lq~qv~~L~~e~~~L--------------~~ei~eLk~  148 (235)
                      ..+|+++.++++.  -|..   -.++++||.-   |=+|++ ++.+.+.|+.+.+.+              +.+++.++.
T Consensus        35 ~~vd~km~ei~~~~~~~~l---~~~r~aVLaALNiadEl~k-~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~  110 (138)
T 3hnw_A           35 SYINNKITEFNKEESYRRM---SAELRTDMMYLNIADDYFK-AKKMADSLSLDIENKDKEIYDLKHELIAAQIKAESSAK  110 (138)
T ss_dssp             HHHHHHHHHHTTCHHHHTS---CHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCCC---CHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999976  5533   4688888653   333333 344444444433333              333333444


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          149 EKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       149 EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      ++.+|++++..|..++-+||..++
T Consensus       111 e~~~l~~~~~~l~~~~~~le~~~~  134 (138)
T 3hnw_A          111 EIKELKSEINKYQKNIVKLETELN  134 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444444444444443

>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=96.02  E-value=0.0091  Score=43.70  Aligned_cols=42  Identities=17%  Similarity=0.238  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          118 AVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQR  159 (235)
Q Consensus       118 AIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~  159 (235)
                      --.||++|..++..|+..+..|..++..|+.++..|+.|+..
T Consensus        27 K~~~i~~LE~~v~~le~~~~~l~~en~~Lr~~i~~L~~El~~   68 (70)
T 1gd2_E           27 KEDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRI   68 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356888888888888877776665555555555555544443

>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=95.44  E-value=0.055  Score=42.28  Aligned_cols=57  Identities=23%  Similarity=0.439  Sum_probs=35.5

Q ss_pred             CCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          108 KTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEK-------IKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       108 K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~e-------i~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      .++|..++.+   ||. |...+..|++++..|+..       |.+|..|...|+.||+.|+.|.+-..
T Consensus        29 ~mSKqELIqE---Yl~-LE~~~s~le~e~~rlr~~~~~~~~~v~eLe~everL~~ENq~L~~e~~~~~   92 (104)
T 3s9g_A           29 NMSKQELIKE---YLE-LEKSLSRMEDENNRLRLESKRLDARVRELELELDRLRAENLQLLTENELHR   92 (104)
T ss_dssp             TSCHHHHHHH---HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHH---HHH-HHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3688888775   444 777777787777777764       45555555555555555555544433

>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=95.42  E-value=0.023  Score=39.35  Aligned_cols=38  Identities=18%  Similarity=0.340  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHH-------HHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 026646          117 DAVQMMEQLRT-------EAQKLKQSNENLQEKIKELKAEKNELR  154 (235)
Q Consensus       117 dAIeYIk~Lq~-------qv~~L~~e~~~L~~ei~eLk~EknELr  154 (235)
                      +|++||++--.       .++.|+.+++.|+.++..|+.+..||+
T Consensus         2 ~AlefIk~~LG~~~p~~~d~eaLk~E~~eLk~k~~~L~~~~~el~   46 (53)
T 2yy0_A            2 SALDFLKHHLGAATPENPEIELLRLELAEMKEKYEAIVEENKKLK   46 (53)
T ss_dssp             --------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68899987533       455666666666555555555554444

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=95.14  E-value=0.16  Score=42.22  Aligned_cols=87  Identities=14%  Similarity=0.089  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646           86 RRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKE  165 (235)
Q Consensus        86 RRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e  165 (235)
                      =|+.|-.+|.+|-.-+-.+. + ..=+|=+.+-..-|..|+.+...|+.++..|.+++++-......|+||...|..+..
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 DRNDKEAHLNELFQDNSGAI-G-GNIVSHDDALLNTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENN  113 (152)
T ss_dssp             -----------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHHHHHhhccCC-C-cccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46666666666665542221 1 112233344455666666666666666666666666665666678888888888887


Q ss_pred             HHHHHHHhc
Q 026646          166 KLEQQVKAM  174 (235)
Q Consensus       166 ~le~qlk~~  174 (235)
                      -++..++.+
T Consensus       114 ~lE~kl~kL  122 (152)
T 3a7p_A          114 VLQQKLSDL  122 (152)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            777777653

>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=95.04  E-value=0.054  Score=37.83  Aligned_cols=35  Identities=26%  Similarity=0.360  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNEL  153 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknEL  153 (235)
                      -.|+.+|+.++..|+.+|..|..+|..|+.|...|
T Consensus        21 k~~~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~L   55 (61)
T 1t2k_D           21 KVWVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQL   55 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35666666666666666666555555444443333

>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=95.02  E-value=0.11  Score=40.43  Aligned_cols=56  Identities=27%  Similarity=0.475  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH----------------------------HHHHHHHHHHHHHHHHHHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEK----------------------------NELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~Ek----------------------------nELr~E~~~Lk~e~e~le~ql  171 (235)
                      +-+..|+.+++.|+.++..|.++++.|..++                            ...+.+...|.+|+++|...|
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            3455677777777777777777766666544                            234456667777777777777


Q ss_pred             Hhcc
Q 026646          172 KAMS  175 (235)
Q Consensus       172 k~~~  175 (235)
                      +.|.
T Consensus        92 ~~lE   95 (100)
T 1go4_E           92 RAME   95 (100)
T ss_dssp             TTCC
T ss_pred             HHHh
Confidence            7664

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

Probab=94.95  E-value=0.18  Score=40.84  Aligned_cols=48  Identities=23%  Similarity=0.293  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEK  166 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~  166 (235)
                      -.-|..|+.++..++..++.+..++.+|+.++++|+.++..|.++.+.
T Consensus        88 ~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~~~  135 (138)
T 3hnw_A           88 DKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETELND  135 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344555666666777777778888888888888888888888776653

>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=94.69  E-value=0.1  Score=38.52  Aligned_cols=47  Identities=19%  Similarity=0.206  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      |.+||..+++..+++....+.|++|..+..+..++...|+.++++++
T Consensus        21 i~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKfr   67 (72)
T 3nmd_A           21 LRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDKYR   67 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            88899988888888888888899999999999999999999888874

>2oqq_A Transcription factor HY5; homodimer leucine zipper; 2.00A {Arabidopsis thaliana}

Probab=94.47  E-value=0.1  Score=34.75  Aligned_cols=35  Identities=26%  Similarity=0.519  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELR  154 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr  154 (235)
                      .|+.+|..++..|+..+.+|.+++.-|..|..-||
T Consensus         3 aYl~eLE~r~k~le~~naeLEervstLq~EN~mLR   37 (42)
T 2oqq_A            3 AYLSELENRVKDLENKNSELEERLSTLQNENQMLR   37 (42)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence            49999999999999999999998888877766666

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=94.47  E-value=0.27  Score=37.31  Aligned_cols=54  Identities=20%  Similarity=0.471  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQ------------EKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~------------~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      |+-|+.|.++...|+.+...++            .+|.+|+..+..+..|+.+|..+++.|+..+.
T Consensus        22 IdKVR~LEqqN~~Le~~i~~l~~~~~~~~~~~ye~~i~~Lr~~i~~~~~ek~~l~~e~dnl~~~~~   87 (93)
T 3s4r_A           22 IDKVRFLEQQNKILLAELEQLKGQGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAEDIM   87 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556777777777776655443            33556666666666666666666666666554

>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=94.30  E-value=0.061  Score=37.75  Aligned_cols=35  Identities=20%  Similarity=0.376  Sum_probs=20.3

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNEL  153 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknEL  153 (235)
                      .+|+.+|+.++..|+.+|..|..++..|..|...|
T Consensus        21 k~~~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~~L   55 (62)
T 1jnm_A           21 LERIARLEEKVKTLKAQNSELASTANMLREQVAQL   55 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45666666666666666666665555554444433

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

Probab=93.63  E-value=0.17  Score=35.84  Aligned_cols=18  Identities=39%  Similarity=0.599  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHhHHHHH
Q 026646          124 QLRTEAQKLKQSNENLQE  141 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~  141 (235)
                      .|+.+++.|+.+|..|..
T Consensus        27 ~le~~~~~L~~~N~~L~~   44 (63)
T 1ci6_A           27 ALTGECKELEKKNEALKE   44 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            333333333333333333

>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA complex, transcription factor, BZIP, C/EBP; 1.80A {Homo sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A 1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A

Probab=93.56  E-value=0.58  Score=34.65  Aligned_cols=55  Identities=16%  Similarity=0.259  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      +|...-+.-...-+.+.+.-.....++.....+|..||..|+.+++.|+.++..+
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            4444433333334444444444555555566666666666666666666666554

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=93.25  E-value=0.64  Score=34.92  Aligned_cols=57  Identities=23%  Similarity=0.370  Sum_probs=49.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          117 DAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       117 dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +=|.-|++|+-+|.+|+.+.-+-.-+++.-+.|...|+.....-.+++++|+.+|-+
T Consensus        23 ~L~qEi~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l~~   79 (81)
T 3qh9_A           23 ELLQELRHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQLSR   79 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHHhh
Confidence            567778999999999999988888888888888888998888888999999998864

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=93.07  E-value=1.1  Score=35.38  Aligned_cols=74  Identities=20%  Similarity=0.321  Sum_probs=40.3

Q ss_pred             HhcCCCCCCCCCchhhH------HHHHHHHHHHHHHHHHHHHHHhHHHHH---HHHHHHHHHHHHHH-------HHHHHH
Q 026646           98 GSMLEPGRPPKTDKATI------LSDAVQMMEQLRTEAQKLKQSNENLQE---KIKELKAEKNELRD-------EKQRLK  161 (235)
Q Consensus        98 rslLP~~~~~K~dKasI------L~dAIeYIk~Lq~qv~~L~~e~~~L~~---ei~eLk~EknELr~-------E~~~Lk  161 (235)
                      +.+||-+  .++++.-|      |..|=+-+..-+.++.+|+.+..++..   .|.-|++...-.++       .-.++.
T Consensus        12 ~~~~~~~--~~~~~~ei~~L~~~L~~AEeaL~~Kq~~idelk~ei~q~~~~lE~I~vLkaQv~IY~~DF~aERadREkl~   89 (110)
T 2v4h_A           12 SGLVPRG--SHMASMQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERHAREKLV   89 (110)
T ss_dssp             -CCCCTT--CCSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCcch--hHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccchhhHHHHH
Confidence            4567755  67777755      455555566666666666666655554   45555554433222       222455


Q ss_pred             HHHHHHHHHHHh
Q 026646          162 ADKEKLEQQVKA  173 (235)
Q Consensus       162 ~e~e~le~qlk~  173 (235)
                      .+|+.|+.||..
T Consensus        90 ~eKe~L~~ql~~  101 (110)
T 2v4h_A           90 EKKEYLQEQLEQ  101 (110)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHH
Confidence            555555555544

>1deb_A APC protein, adenomatous polyposis coli protein; coiled coil, tumor suppressor, structural protein; 2.40A {Homo sapiens} SCOP: h.1.18.1

Probab=93.06  E-value=0.33  Score=33.70  Aligned_cols=46  Identities=24%  Similarity=0.393  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      .+|-+||+.|+.||..|+.+++.=....+.|..|...+|.=...|+
T Consensus         6 dQL~~QVe~Lk~ENshLrrEL~dNS~~lskLE~ets~mKevlk~lq   51 (54)
T 1deb_A            6 DQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQ   51 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHc
Confidence            4678899999999999998888877778888888777766555554

>3cve_A Homer protein homolog 1; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, postsynaptic cell membrane, synapse; 1.75A {Rattus norvegicus}

Probab=92.98  E-value=0.42  Score=35.14  Aligned_cols=50  Identities=12%  Similarity=0.294  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      +.+.++.+.++.+|..|+.++..|+...++-+.+-..++.|+.++-++|.
T Consensus         3 ~~~~~kLq~~E~~N~~Le~~v~~le~~Le~s~~~q~~~~~Elk~~~e~Ld   52 (72)
T 3cve_A            3 HNSHMKLQEVEIRNKDLEGQLSEMEQRLEKSQSEQDAFRSNLKTLLEILD   52 (72)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45667778888888888888888888888888777777777777766654

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

Probab=92.66  E-value=0.62  Score=36.78  Aligned_cols=51  Identities=31%  Similarity=0.421  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAE----KNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~E----knELr~E~~~Lk~e~e~le~qlk  172 (235)
                      ++.|+..+.+|..+++.++.+.+..+.+    .+.|++|...|+...+.+...|.
T Consensus         5 ~rdL~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iR   59 (111)
T 2v66_B            5 NRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVR   59 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666666666666665554444332    33444444444444444444433

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1

Probab=92.54  E-value=0.48  Score=32.91  Aligned_cols=37  Identities=22%  Similarity=0.346  Sum_probs=23.9

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          135 SNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       135 e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      ....|+.++..|+.+..+|+.+...|+.|+..|.++|
T Consensus        23 ~~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~Lk~~l   59 (61)
T 1t2k_D           23 WVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLKQLL   59 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3455666666666666666666666666666666655

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=92.52  E-value=0.11  Score=35.99  Aligned_cols=29  Identities=28%  Similarity=0.454  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKA  148 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~  148 (235)
                      .||.+|..+|..|+.+|..|..++..|+.
T Consensus        22 ~~~~~LE~~v~~L~~eN~~L~~~~~~L~~   50 (55)
T 1dh3_A           22 EYVKSLENRVAVLENQNKTLIEELKALKD   50 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56666666666666666666665555543

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=92.33  E-value=0.95  Score=34.17  Aligned_cols=28  Identities=29%  Similarity=0.426  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          145 ELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       145 eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      ++..+..+|..||..|+.+++.|+.++.
T Consensus        40 e~~~r~~~Le~EN~~Lr~~v~~L~~E~~   67 (87)
T 1hjb_A           40 ETQHKVLELTAENERLQKKVEQLSRELS   67 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333334444444444444444444433

>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=92.21  E-value=1.1  Score=34.11  Aligned_cols=40  Identities=15%  Similarity=0.362  Sum_probs=28.0

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          135 SNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       135 e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      +...|+.+...|..++..|+.|+..+..|++.+.+.+.++
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            3455666666677777777777777777777777777665

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

Probab=92.17  E-value=0.94  Score=31.89  Aligned_cols=45  Identities=29%  Similarity=0.357  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          118 AVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKA  162 (235)
Q Consensus       118 AIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~  162 (235)
                      |.+|=..=+.+.+.|+.+.+.|..+..+|+.+.+.|+.|+..|+.
T Consensus        14 A~R~R~KKk~~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~Lk~   58 (63)
T 1ci6_A           14 ATRYRQKKRAEQEALTGECKELEKKNEALKERADSLAKEIQYLKD   58 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444455555555555555555555555555555544443

>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=92.09  E-value=0.5  Score=44.34  Aligned_cols=12  Identities=8%  Similarity=0.202  Sum_probs=5.8

Q ss_pred             hHHHHHHHHHHH
Q 026646          113 TILSDAVQMMEQ  124 (235)
Q Consensus       113 sIL~dAIeYIk~  124 (235)
                      ..|.+.+..+++
T Consensus       505 ~~l~~~~~~~~~  516 (597)
T 3oja_B          505 DNLNKVFTHLKE  516 (597)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            445555544443

>3he5_B Synzip2; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=92.00  E-value=0.5  Score=31.98  Aligned_cols=42  Identities=31%  Similarity=0.423  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKE  165 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e  165 (235)
                      .|+..+.+|++.|-+|+..-+.|..-+..||+|..+|..|.-
T Consensus         7 ylrkkiarlkkdnlqlerdeqnlekiianlrdeiarleneva   48 (52)
T 3he5_B            7 YLRKKIARLKKDNLQLERDEQNLEKIIANLRDEIARLENEVA   48 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHHHHHHHHHh
Confidence            467788888888888776666677667778877777766653

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

Probab=91.75  E-value=0.88  Score=34.64  Aligned_cols=47  Identities=23%  Similarity=0.507  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      ..|+.+++.|+.+-..|..++..|..+...+..+...+..+.++|.+
T Consensus         7 ~~l~~eL~~l~~eE~~L~~eL~~lEke~~~l~~el~~le~E~~~L~~   53 (96)
T 3q8t_A            7 EQLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQ   53 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhh
Confidence            44555555555555555555555555555555555555555555544

>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=91.68  E-value=1.8  Score=29.37  Aligned_cols=52  Identities=13%  Similarity=0.188  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +..|+..+..++.....+..++..++...+.+..+......+|.+++.|++.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi~~   58 (60)
T 3htk_A            7 KKTLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEY   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4555666666655555566666666666666666666666777777666654

>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=91.50  E-value=0.25  Score=35.07  Aligned_cols=31  Identities=23%  Similarity=0.442  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          141 EKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       141 ~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      ..+.+|..+..+|..+|..|+++++.|.++|
T Consensus        30 ~~~~~Le~~v~~L~~eN~~L~~ev~~Lr~~l   60 (63)
T 2dgc_A           30 QRMKQLEDKVEELLSKNYHLENEVARLKKLV   60 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444555555555555555555555544

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

Probab=91.36  E-value=1.3  Score=37.79  Aligned_cols=55  Identities=33%  Similarity=0.399  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHH
Q 026646          118 AVQMMEQLRTEAQKLKQSNENLQEKIKELKAE----KNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       118 AIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~E----knELr~E~~~Lk~e~e~le~qlk  172 (235)
                      +=.-++.|+.++..|..+++.++.+.+....+    .+.|++|.+.|+..++.+...|.
T Consensus        54 ~Ek~~~~L~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~el~~l~~~~~~l~~~ir  112 (189)
T 2v71_A           54 AEQRNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVR  112 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33445556666666666666555555444444    55555566666555555555544

>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D

Probab=90.97  E-value=0.99  Score=31.63  Aligned_cols=37  Identities=35%  Similarity=0.466  Sum_probs=22.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          136 NENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       136 ~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      ...|+.++..|+.+..+|+.+...|..++..|...|.
T Consensus        25 ~~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk~~l~   61 (63)
T 2wt7_A           25 TDTLQAETDQLEDEKSALQTEIANLLKEKEKLEFILA   61 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555666666666666666666666666665554

>3cvf_A Homer-3, homer protein homolog 3; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, phosphoprotein, polymorphism; 2.90A {Homo sapiens}

Probab=90.53  E-value=0.84  Score=34.04  Aligned_cols=48  Identities=21%  Similarity=0.407  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      +.++++.++.+|..|+.+++.|+...++-+.+-..++.|+.++-++|.
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            445667777777777777777777777777777777777777666654

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=90.40  E-value=0.29  Score=43.63  Aligned_cols=25  Identities=12%  Similarity=0.292  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhccCCCC
Q 026646          155 DEKQRLKADKEKLEQQVKAMSAPSG  179 (235)
Q Consensus       155 ~E~~~Lk~e~e~le~qlk~~~~~p~  179 (235)
                      ++...++.|+++|+.||+.+.+||.
T Consensus        75 ~~Lk~ar~El~~LkeElerL~sPPL   99 (251)
T 3m9b_A           75 ETLKEARQQLLALREEVDRLGQPPS   99 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSCCE
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            3334445566666666666677774

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=90.21  E-value=2  Score=36.20  Aligned_cols=52  Identities=19%  Similarity=0.407  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          117 DAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       117 dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      .+-+.|.+|+.++..|..+++.+......+..++..|.+....|..++..++
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            3455666666666666666666666666666666666666666655555555

>3swf_A CGMP-gated cation channel alpha-1; coiled-coil, assembly domain, transport protein; 2.14A {Bos taurus}

Probab=90.21  E-value=1  Score=33.32  Aligned_cols=49  Identities=24%  Similarity=0.345  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      +.|...|.+|+...+.|+.+...|-+|..   .-..+||..+.+||.+++..
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            35778888899988889888888866554   44478999999999999973

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=90.03  E-value=0.54  Score=35.55  Aligned_cols=26  Identities=31%  Similarity=0.495  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHH
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAE  149 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~E  149 (235)
                      +++.++..|+.+|..|+.+|..|+.|
T Consensus        40 e~~~r~~~Le~EN~~Lr~~v~~L~~E   65 (87)
T 1hjb_A           40 ETQHKVLELTAENERLQKKVEQLSRE   65 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555444333

>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=90.01  E-value=1.5  Score=42.89  Aligned_cols=52  Identities=17%  Similarity=0.200  Sum_probs=37.7

Q ss_pred             HHHHHHHHHH-HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          114 ILSDAVQMME-QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKE  165 (235)
Q Consensus       114 IL~dAIeYIk-~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e  165 (235)
                      =+..++.-|. +|+++++.|+.++......|+.|+.-+.+++.+.++|..+|.
T Consensus       103 dNdNtynE~S~ELRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvDId  155 (562)
T 3ghg_A          103 NRDNTYNRVSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDID  155 (562)
T ss_dssp             HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444 888888888887766567788888888888888888877764

>3m91_A Proteasome-associated ATPase; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis} PDB: 3m9h_A

Probab=89.94  E-value=1.4  Score=30.31  Aligned_cols=40  Identities=25%  Similarity=0.410  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          121 MMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKL  167 (235)
Q Consensus       121 YIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~l  167 (235)
                      -+.+|+.++..|...|++|.+..       .+.|++...|+.++++|
T Consensus        10 r~~~l~~~l~~L~~rN~rL~~~L-------~~AR~el~~Lkeele~L   49 (51)
T 3m91_A           10 DIHQLEARIDSLAARNSKLMETL-------KEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHh
Confidence            34456666666666666655444       44555556666666655

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=89.87  E-value=0.41  Score=42.68  Aligned_cols=38  Identities=18%  Similarity=0.309  Sum_probs=22.6

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          131 KLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       131 ~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      +|+.++..|..+.++|+.+.+++++|...||.|+++|.
T Consensus        58 eL~~ql~~L~arNe~L~~~Lk~ar~El~~LkeElerL~   95 (251)
T 3m9b_A           58 QLEARIDSLAARNSKLMETLKEARQQLLALREEVDRLG   95 (251)
T ss_dssp             HHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34444444444444555566666777777777777764

>3swy_A Cyclic nucleotide-gated cation channel alpha-3; coiled-coil, assembly domain, transport protein; 1.90A {Homo sapiens}

Probab=89.80  E-value=1.4  Score=29.80  Aligned_cols=45  Identities=31%  Similarity=0.414  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      +|...|++|+...+.|+.+...|-+|..   .--.+||..+.+||.++
T Consensus         2 dlEekv~~Le~~ld~LqTr~ArLlae~~---ssq~KlKqRit~lE~~v   46 (46)
T 3swy_A            2 ALEEKVEQLGSSLDTLQTRFARLLAEYN---ATQMKMKQRLSQLESQV   46 (46)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcC
Confidence            4677888888888888888877765544   44478999999998764

>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=89.72  E-value=0.64  Score=32.39  Aligned_cols=30  Identities=23%  Similarity=0.385  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          143 IKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       143 i~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      +.+|..+..+|..+|..|+.++..|+.++.
T Consensus        24 ~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~   53 (62)
T 1jnm_A           24 IARLEEKVKTLKAQNSELASTANMLREQVA   53 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444443

>3m91_A Proteasome-associated ATPase; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis} PDB: 3m9h_A

Probab=89.64  E-value=1.2  Score=30.64  Aligned_cols=39  Identities=18%  Similarity=0.338  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          137 ENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       137 ~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      ..|+.++..|......|-+-....+.+|.+|..+|..++
T Consensus        12 ~~l~~~l~~L~~rN~rL~~~L~~AR~el~~Lkeele~La   50 (51)
T 3m91_A           12 HQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRLG   50 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            345555555655555677777777777777777777654

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=89.45  E-value=1.6  Score=34.69  Aligned_cols=67  Identities=19%  Similarity=0.337  Sum_probs=32.9

Q ss_pred             CCchhhHHHHHHHHHHHHHHHHHHHHHHh----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          108 KTDKATILSDAVQMMEQLRTEAQKLKQSN----ENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       108 K~dKasIL~dAIeYIk~Lq~qv~~L~~e~----~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      +.+|-.++..=-.-|..|+.+++.++.+.    .+|+..|..|..+..+-+.+++....|.+.|..++..+
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            33444333333333333444444433322    24444455555555555555555566666666666654

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.95  E-value=0.46  Score=44.63  Aligned_cols=45  Identities=18%  Similarity=0.347  Sum_probs=31.8

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 026646          135 SNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSG  179 (235)
Q Consensus       135 e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~~p~  179 (235)
                      ...+|+.+++.|..+.+.+++|...++.+..+++.+++.+..+|.
T Consensus        50 ~lk~le~~~~~L~~e~e~l~~~~~~~~~e~~~~~ee~~~l~~~~~   94 (428)
T 4b4t_K           50 KLKKLEKEYELLTLQEDYIKDEQRHLKRELKRAQEEVKRIQSVPL   94 (428)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSCE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence            334455555566666667777777888888888888888877664

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=88.82  E-value=4.8  Score=31.87  Aligned_cols=50  Identities=16%  Similarity=0.278  Sum_probs=34.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          111 KATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKL  167 (235)
Q Consensus       111 KasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~l  167 (235)
                      --.|..++=.||.+|+.++..|+.+++.-+..       +.+...|+..|+.+++.+
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 LENMKTESQRVVLQLKGHVSELEADLAEQQHL-------RQQAADDCEFLRAELDEL   80 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH
Confidence            34578899999999999999999888765544       344445555555555544

>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1

Probab=88.80  E-value=1.1  Score=32.48  Aligned_cols=39  Identities=18%  Similarity=0.304  Sum_probs=25.4

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          135 SNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       135 e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ....|+.++.+|..+...|..|+..|+.+++.|..+++.
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            344555556666666666677777777777777777654

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=88.75  E-value=2.5  Score=31.94  Aligned_cols=33  Identities=21%  Similarity=0.402  Sum_probs=13.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          136 NENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       136 ~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      ...|+.+|..+..++..|.-|...|..+++++.
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            334444444444444444444444444444433

>1ik9_A DNA repair protein XRCC4; DNA END joining, double-strand break repair, V(D)J recombination, protein-protein complex, coiled coil; HET: DNA; 2.30A {Homo sapiens} SCOP: b.59.1.1 h.1.11.1 PDB: 3ii6_A* 1fu1_A* 3rwr_A*

Probab=88.69  E-value=2.5  Score=36.40  Aligned_cols=41  Identities=12%  Similarity=0.264  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 026646          115 LSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRD  155 (235)
Q Consensus       115 L~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~  155 (235)
                      +.=+++-+..|++++..|..+++.|+.+++.|..+..++-.
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            56666666666666666666666666555555554444433

>3he5_A Synzip1; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=88.59  E-value=2.1  Score=28.58  Aligned_cols=23  Identities=35%  Similarity=0.583  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEK  142 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~e  142 (235)
                      ..+.+|..++..|+.+|+.|..+
T Consensus         3 nlvaqlenevaslenenetlkkk   25 (49)
T 3he5_A            3 NLVAQLENEVASLENENETLKKK   25 (49)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhhcccHHHHHh
Confidence            35678888899998888887654

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=88.33  E-value=1.2  Score=41.36  Aligned_cols=53  Identities=21%  Similarity=0.334  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      |..|+.+++.|+++..+|+++|+.++.+..++.+..........+|..+|..+
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            45677777777777777777777777777777766665555556666666554

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=88.25  E-value=3.6  Score=38.45  Aligned_cols=15  Identities=27%  Similarity=0.372  Sum_probs=5.8

Q ss_pred             HHHHHHHHHHHHHHh
Q 026646          159 RLKADKEKLEQQVKA  173 (235)
Q Consensus       159 ~Lk~e~e~le~qlk~  173 (235)
                      .++.|...+.++++.
T Consensus       562 ~l~~e~~~~~~~~~~  576 (597)
T 3oja_B          562 ELRQETSLKRQKVKQ  576 (597)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            333333333333433

>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=87.79  E-value=1.5  Score=33.97  Aligned_cols=43  Identities=26%  Similarity=0.400  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCC
Q 026646          141 EKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPH  183 (235)
Q Consensus       141 ~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~~~p~~~p~  183 (235)
                      +++..|+.++.+|+.|+.+|+.+|+.|+-+|......-.|-|.
T Consensus        12 e~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~~l~Gd~~~~   54 (100)
T 1go4_E           12 EEADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQGDYDQS   54 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCSCCCTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCc
Confidence            4667788888888888888889999999999887665556553

>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=87.79  E-value=1.5  Score=32.35  Aligned_cols=33  Identities=30%  Similarity=0.414  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELR  154 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr  154 (235)
                      ..+++.++..|+.+|..|+.+|..|+.|...|+
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            345666777777777777777766665555444

>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=87.76  E-value=3.3  Score=28.05  Aligned_cols=50  Identities=24%  Similarity=0.253  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          117 DAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEK  166 (235)
Q Consensus       117 dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~  166 (235)
                      ..-+++..+..++..++.+...+...+..+..+.+..+++...++.+++.
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi~~   58 (60)
T 3htk_A            9 TLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEY   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44566777777888888888888888899999999999999999888865

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

Probab=87.64  E-value=1  Score=32.71  Aligned_cols=33  Identities=27%  Similarity=0.440  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          143 IKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       143 i~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      |+.|..+..+|..|+..|+.+++.|+++|.++.
T Consensus        49 I~~L~~~~~~l~~e~~~L~~~~~~L~~~l~~L~   81 (83)
T 1nkp_B           49 IQYMRRKNHTHQQDIDDLKRQNALLEQQVRALG   81 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            566677777777888888888888888888764

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=87.57  E-value=3.6  Score=34.13  Aligned_cols=79  Identities=20%  Similarity=0.242  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHhcCCC---CCCCCCchhhHHHHHHHHHHHHHHHHHHHH-------HHhHHHHHHHHHHHHHHHHHHHHHH
Q 026646           89 RLNERFLELGSMLEP---GRPPKTDKATILSDAVQMMEQLRTEAQKLK-------QSNENLQEKIKELKAEKNELRDEKQ  158 (235)
Q Consensus        89 kINd~F~eLrslLP~---~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~-------~e~~~L~~ei~eLk~EknELr~E~~  158 (235)
                      +++..|.++..+.++   +. .++... .|..--.-+..|+.++..|+       +.++.|+.++..|..+.|.+.+...
T Consensus        43 ~~~~l~~e~~~~~~~~~vs~-~~~~~~-~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE~kl~  120 (152)
T 3a7p_A           43 HLNELFQDNSGAIGGNIVSH-DDALLN-TLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKLS  120 (152)
T ss_dssp             --------------CHHHHH-HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhccCCCcccccc-hhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355566666666654   00 112222 33333344455555555555       4456777777778888888887777


Q ss_pred             HHHHHHHHHHH
Q 026646          159 RLKADKEKLEQ  169 (235)
Q Consensus       159 ~Lk~e~e~le~  169 (235)
                      .|+.|...|-+
T Consensus       121 kLq~EN~~LV~  131 (152)
T 3a7p_A          121 DLKKEHSQLVA  131 (152)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            77777655433

>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=87.56  E-value=5.2  Score=31.45  Aligned_cols=60  Identities=18%  Similarity=0.351  Sum_probs=31.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          113 TILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       113 sIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      ..+.+|-+....|..+-..|+.....+.+.+.+.....++|..++-.|..++..|+.+|.
T Consensus        62 ~~l~e~EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~Lk~~le  121 (129)
T 2fxo_A           62 DNLADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSELKRDID  121 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445566666666666555555555555555544444444444444445455555544444

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=86.96  E-value=5.9  Score=30.54  Aligned_cols=21  Identities=14%  Similarity=0.211  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHHHhHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQ  140 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~  140 (235)
                      +-|.+|+.++...+.+...|+
T Consensus        12 e~l~~le~~~~~~~~e~~~L~   32 (97)
T 2eqb_B           12 EDYNTLKRELSDRDDEVKRLR   32 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHH
Confidence            333444444433333333333

>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=86.91  E-value=0.96  Score=28.64  Aligned_cols=22  Identities=36%  Similarity=0.548  Sum_probs=8.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 026646          139 LQEKIKELKAEKNELRDEKQRL  160 (235)
Q Consensus       139 L~~ei~eLk~EknELr~E~~~L  160 (235)
                      |++++++|-.++.+|++|..+|
T Consensus         5 LE~kVEeLl~~n~~Le~EV~RL   26 (33)
T 3m48_A            5 LEAKVEELLSKNWNLENEVARL   26 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHH
Confidence            3334444433333333333333

>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=86.68  E-value=7.3  Score=28.23  Aligned_cols=58  Identities=12%  Similarity=0.280  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       116 ~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ..|.+-+.+++.++...+....++.+++..|+..+..|.++...+.......+..|..
T Consensus        16 d~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~ee~l~~a~~kLee   73 (81)
T 1ic2_A           16 ENALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESLKDAQEKLEL   73 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455666666666666666777777777777777777777666666665555555543

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=86.61  E-value=6.2  Score=29.74  Aligned_cols=54  Identities=15%  Similarity=0.284  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       116 ~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      ..|++-..+++.++..++..+.++.+++..|+..+..|.++...+.........
T Consensus        19 e~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~eld~~~e~l~~a~~   72 (101)
T 3u59_A           19 ENAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEKYSESVKEAQE   72 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456777777777777777777777777777766666666655544444443333

>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=86.57  E-value=3.1  Score=29.32  Aligned_cols=32  Identities=28%  Similarity=0.403  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 026646          118 AVQMMEQLRTEAQKLKQSNENLQEKIKELKAE  149 (235)
Q Consensus       118 AIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~E  149 (235)
                      -.+|+.+|+.++..|+.+|..|..++..|+.+
T Consensus        28 K~~~~~~Le~~v~~L~~eN~~L~~ev~~Lr~~   59 (63)
T 2dgc_A           28 KLQRMKQLEDKVEELLSKNYHLENEVARLKKL   59 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45677778888888877777777776666544

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=86.49  E-value=3.7  Score=30.58  Aligned_cols=31  Identities=16%  Similarity=0.310  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          139 LQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       139 L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      |+.+|..|+.|+.+||-.+..+.-+++.+.+
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            3344444444444444444444444444333

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=86.28  E-value=2.3  Score=31.25  Aligned_cols=50  Identities=14%  Similarity=0.104  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      |..++.+|+....-+...|++|....-+-..+...|..++..|..+|+.+
T Consensus        12 le~Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L~~rl~~~   61 (78)
T 3efg_A           12 LEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKV   61 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34444444444444444444444444444444444444444454444443

>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=86.22  E-value=1.1  Score=28.53  Aligned_cols=24  Identities=38%  Similarity=0.531  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          138 NLQEKIKELKAEKNELRDEKQRLK  161 (235)
Q Consensus       138 ~L~~ei~eLk~EknELr~E~~~Lk  161 (235)
                      +|..++++|-.++.+|++|..+|+
T Consensus         5 QLE~kVEeLl~~n~~Le~eV~rLk   28 (34)
T 2oxj_A            5 QLEXKVXELLXKNXHLEXEVXRLK   28 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHH
Confidence            444555555555555555555444

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

Probab=86.19  E-value=2.5  Score=44.05  Aligned_cols=16  Identities=38%  Similarity=0.690  Sum_probs=6.6

Q ss_pred             HHHHHHHHHHHHHHHH
Q 026646          153 LRDEKQRLKADKEKLE  168 (235)
Q Consensus       153 Lr~E~~~Lk~e~e~le  168 (235)
                      |++|++.|+++++.|+
T Consensus      1028 L~~e~~~L~qq~~~l~ 1043 (1080)
T 2dfs_A         1028 LKEQNTLLKTEKEELN 1043 (1080)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3334444444444444

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

Probab=86.15  E-value=7.2  Score=29.57  Aligned_cols=46  Identities=15%  Similarity=0.316  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLK  161 (235)
Q Consensus       116 ~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk  161 (235)
                      ..|++-..+++.++..++..+.++.++|..|...+..|.++...+.
T Consensus        19 e~a~drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~eld~~e   64 (101)
T 3u1c_A           19 ENALDRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTEDSRDQVL   64 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            3466666666666666666666666666666655555555444333

>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=86.09  E-value=2.7  Score=30.00  Aligned_cols=36  Identities=25%  Similarity=0.504  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          126 RTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLK  161 (235)
Q Consensus       126 q~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk  161 (235)
                      ..++++|-+-|..|.++++-|..+.+.|+.|+..|+
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            446777777888888888888888888888888775

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

Probab=86.04  E-value=2.9  Score=43.58  Aligned_cols=22  Identities=14%  Similarity=0.184  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhc
Q 026646          153 LRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       153 Lr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      |++....|+.++.+|++|+..+
T Consensus      1021 L~~kv~~L~~e~~~L~qq~~~l 1042 (1080)
T 2dfs_A         1021 TEQLVSELKEQNTLLKTEKEEL 1042 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3344446666666677766554

>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=85.90  E-value=1.9  Score=27.76  Aligned_cols=26  Identities=27%  Similarity=0.511  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          138 NLQEKIKELKAEKNELRDEKQRLKAD  163 (235)
Q Consensus       138 ~L~~ei~eLk~EknELr~E~~~Lk~e  163 (235)
                      +|..++++|-.++.+|.+|..+|+..
T Consensus         5 QLE~kVEeLl~~~~~Le~EV~RL~~l   30 (36)
T 1kd8_A            5 QLEAEVEEIESEVWHLENEVARLEKE   30 (36)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            34444444545555555555544443

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=85.76  E-value=15  Score=33.64  Aligned_cols=33  Identities=15%  Similarity=0.245  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          141 EKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       141 ~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      ...+....+.+.|++|+++++.+++.+..++..
T Consensus       435 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  467 (487)
T 3oja_A          435 RDWDMYQHKETQLAEENARLKKLNGEADLALAS  467 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHhhhhhhhhhhhhhhhHh
Confidence            334444555556666666666666666665554

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=85.70  E-value=5.3  Score=29.71  Aligned_cols=39  Identities=13%  Similarity=0.199  Sum_probs=16.6

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          135 SNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       135 e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      .++.|+.+|..|+-...++.-+...++..-..+.+.|..
T Consensus        28 Ql~~Lq~Ev~~LRGqiE~~~~~l~ql~~rQrd~Y~dLD~   66 (83)
T 2xdj_A           28 QLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDS   66 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444444444444444444444444443

>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=85.70  E-value=3.3  Score=28.68  Aligned_cols=51  Identities=22%  Similarity=0.322  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      +++++..+..|+.+..+++.++.....|+.+|-+=|..|..||.--..-|.
T Consensus         2 l~~~q~~i~~le~el~~~r~e~~~q~~eYq~LlniK~~Le~EIatYRkLLE   52 (59)
T 1gk6_A            2 MKQLEDKVEELLSKNYHLENEVARLKKLVGDLLNVKMALDIEIATYRKLLE   52 (59)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHc
Confidence            356788888888888889888888888999999999999988877665554

>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=85.70  E-value=6.9  Score=30.70  Aligned_cols=47  Identities=23%  Similarity=0.384  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          126 RTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       126 q~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      ......|......|..+++++.....+..+.+..|.+++.++++++.
T Consensus        68 EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~  114 (129)
T 2fxo_A           68 EERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECS  114 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444555555555555555555555555555555555544

>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=85.67  E-value=5.2  Score=34.37  Aligned_cols=38  Identities=18%  Similarity=0.307  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEK  157 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~  157 (235)
                      +-+..|+.++++|+.+..+|..+++++..+|+++..+.
T Consensus       139 ~~~~~L~~e~~~l~~~~~~l~~qlE~~v~~K~~~E~~L  176 (213)
T 1ik9_A          139 AKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDL  176 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33455566666677766667667666666666665543

>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=85.30  E-value=1.3  Score=28.00  Aligned_cols=24  Identities=17%  Similarity=0.382  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          138 NLQEKIKELKAEKNELRDEKQRLK  161 (235)
Q Consensus       138 ~L~~ei~eLk~EknELr~E~~~Lk  161 (235)
                      +|+.++++|-.++.+|++|..+||
T Consensus         4 QLEdKvEeLl~~~~~Le~EV~RLk   27 (33)
T 3c3g_A            4 XIEXKLXEIXSKXYHXENXLARIK   27 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHH
Confidence            344555555555555555555554

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=85.24  E-value=5.2  Score=31.21  Aligned_cols=51  Identities=12%  Similarity=0.173  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      .-|+...+.+++...+++.+.++...+.+.++-....|+.++..++.+|+.
T Consensus        33 dlLKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~~lk~~L~q   83 (103)
T 4h22_A           33 DTLKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEVKEALKQ   83 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444555555555555555555555555555555666666666666665

>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=85.19  E-value=1.6  Score=29.93  Aligned_cols=25  Identities=20%  Similarity=0.457  Sum_probs=9.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          146 LKAEKNELRDEKQRLKADKEKLEQQ  170 (235)
Q Consensus       146 Lk~EknELr~E~~~Lk~e~e~le~q  170 (235)
                      |+.|..+|+.+...|+.+++.+..+
T Consensus        24 Lk~E~~eLk~k~~~L~~~~~el~~~   48 (53)
T 2yy0_A           24 LRLELAEMKEKYEAIVEENKKLKAK   48 (53)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333333

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

Probab=85.01  E-value=4.3  Score=35.04  Aligned_cols=30  Identities=13%  Similarity=0.148  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          142 KIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       142 ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      ++.+++.++..+..+...++..+++.+.++
T Consensus        54 ~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l   83 (256)
T 3na7_A           54 EKLALKLQVSKNEQTLQDTNAKIASIQKKM   83 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333333333

>3vmx_A Voltage-gated hydrogen channel 1; coiled-coil, ION channel, ION transport, membrane protein; 1.45A {Mus musculus}

Probab=84.95  E-value=2.9  Score=28.51  Aligned_cols=42  Identities=26%  Similarity=0.287  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          126 RTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       126 q~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      ++++.+|++.|.+|-++|.+|       ......+..||+||..-|+.-
T Consensus         3 eq~l~kLKe~n~~L~~kv~~L-------e~~c~~~eQEieRL~~LLkqH   44 (48)
T 3vmx_A            3 ERQILRLKQINIQLATKIQHL-------EFSCSEKEQEIERLNKLLKQN   44 (48)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHccHHHHHHHHHHHHHHHc
Confidence            456778888888876666555       444555668888888887753

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=84.81  E-value=4  Score=31.47  Aligned_cols=49  Identities=16%  Similarity=0.390  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      |+.++.+|+.++.....++..|..+..+-+.-......++.+++++|..
T Consensus        10 lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEe   58 (97)
T 2eqb_B           10 LKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVED   58 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444444433333333223333334444444443

>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=84.38  E-value=1.5  Score=27.70  Aligned_cols=24  Identities=25%  Similarity=0.272  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          138 NLQEKIKELKAEKNELRDEKQRLK  161 (235)
Q Consensus       138 ~L~~ei~eLk~EknELr~E~~~Lk  161 (235)
                      +|+.++++|..++.+|.+|..+|+
T Consensus         4 QLEdKVEell~~~~~le~EV~Rl~   27 (33)
T 2wq1_A            4 QLEDKIEENTSKIYHNTNEIARNT   27 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHH
Confidence            445555555555555555554443

>2wt7_B Transcription factor MAFB; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 2wty_A* 1k1v_A

Probab=84.35  E-value=2  Score=32.65  Aligned_cols=37  Identities=27%  Similarity=0.462  Sum_probs=18.7

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          130 QKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEK  166 (235)
Q Consensus       130 ~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~  166 (235)
                      ..|+.++..|+.+++.|+.|..++..|...+|...+.
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            4455555555555555555555555555555544443

>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=84.18  E-value=7.8  Score=36.44  Aligned_cols=60  Identities=13%  Similarity=0.130  Sum_probs=41.3

Q ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          110 DKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       110 dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      .+......++++++++..++.+|+.......++|+.|+...+.++...+.|+..+..|+.
T Consensus        74 ~~~d~~e~~tq~skkml~~~~~~e~~~~~~~~~i~~l~~~~~~~~~~i~~l~~~i~~l~~  133 (409)
T 1m1j_C           74 TLPQSIEQLTQKSKKIIEEIIRYENTILAHENTIQQLTDMHIMNSNKITQLKQKIAQLES  133 (409)
T ss_dssp             CCSSCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence            344445666999999999999998877777777877777766665555555555544433

>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=84.10  E-value=1.5  Score=28.17  Aligned_cols=23  Identities=39%  Similarity=0.593  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 026646          139 LQEKIKELKAEKNELRDEKQRLK  161 (235)
Q Consensus       139 L~~ei~eLk~EknELr~E~~~Lk  161 (235)
                      |..++++|..++.+|.+|..+|+
T Consensus         6 LE~KVEeLl~~~~~Le~eV~RLk   28 (36)
T 1kd8_B            6 LKAKVEELKSKLWHLKNKVARLK   28 (36)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHH
Confidence            33344444444444444444443

>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=83.99  E-value=3.6  Score=38.43  Aligned_cols=52  Identities=21%  Similarity=0.282  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      ..|+.++.+|++++++|+++++.++.+..++.++......+..+|..+|..+
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            4678888888888888888888888888888777766666667777777765

>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=83.98  E-value=1.6  Score=27.74  Aligned_cols=24  Identities=13%  Similarity=0.339  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          138 NLQEKIKELKAEKNELRDEKQRLK  161 (235)
Q Consensus       138 ~L~~ei~eLk~EknELr~E~~~Lk  161 (235)
                      +|..++++|-.++.+|++|..+||
T Consensus         5 QLEdKVEeLl~~~~~Le~EV~RLk   28 (34)
T 3c3f_A            5 QIEXKLEXILSXLYHXENEXARIX   28 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHH
Confidence            344455555555555555555554

>1jcd_A Major outer membrane lipoprotein; protein folding, coiled coil, helix capping, alanine-zipper, membrane protein; 1.30A {Escherichia coli} SCOP: h.1.16.1 PDB: 1eq7_A 1t8z_A* 2guv_A 2gus_A 1jcc_A 1kfn_A 1kfm_A

Probab=83.96  E-value=6  Score=27.18  Aligned_cols=43  Identities=19%  Similarity=0.282  Sum_probs=21.8

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          129 AQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       129 v~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      +++|......|..++..|+.+.+.|+.+...-|.|-.|-.+-|
T Consensus         6 i~~Lss~V~~L~~kVdqLssdV~al~~~v~~ak~eA~RAN~Rl   48 (52)
T 1jcd_A            6 ADQASSDAQTANAKADQASNDANAARSDAQAAKDDAARANQRA   48 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3444444444444455555555555555555555555554444

>3v86_A De novo design helix; computational design of A protein crystal, helical coil, DE designed helix, de novo protein; 2.91A {Synthetic}

Probab=83.93  E-value=0.99  Score=26.90  Aligned_cols=26  Identities=31%  Similarity=0.497  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHH
Q 026646          121 MMEQLRTEAQKLKQSNENLQEKIKEL  146 (235)
Q Consensus       121 YIk~Lq~qv~~L~~e~~~L~~ei~eL  146 (235)
                      |+-+|+.++-+|+-+...|..++++|
T Consensus         1 yvyqlkdevgelkgevralkdevkdl   26 (27)
T 3v86_A            1 YVYQLKDEVGELKGEVRALKDEVKDL   26 (27)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchhhHHHHHHHhHHHHHHHHHhcc
Confidence            34555555555555555554444443

>1c1g_A Tropomyosin; contractIle protein; 7.00A {Sus scrofa} SCOP: h.1.5.1 PDB: 2tma_A 2w49_A 2w4u_A

Probab=83.87  E-value=8.8  Score=30.57  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 026646          146 LKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       146 Lk~EknELr~E~~~Lk~e~e~le  168 (235)
                      +..+...++.+...+..++.+++
T Consensus       249 ~~~~~~~~~~~~~~~~~~~~~~~  271 (284)
T 1c1g_A          249 LEKSIDDLEDELYAQKLKYKAIS  271 (284)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=83.59  E-value=4.2  Score=27.87  Aligned_cols=32  Identities=19%  Similarity=0.293  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          140 QEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       140 ~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      +.-+.+|..+...|..||..|+.++..|++++
T Consensus        21 k~~~~~LE~~v~~L~~eN~~L~~~~~~L~~~~   52 (55)
T 1dh3_A           21 KEYVKSLENRVAVLENQNKTLIEELKALKDLY   52 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34567777777888888888888888887654

>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=83.58  E-value=10  Score=28.06  Aligned_cols=46  Identities=26%  Similarity=0.437  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          123 EQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      ..|++.-++|..-..+|..-|..|..|.++|......|+...+.|+
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            3455555555555556666666666666666666666655555443

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=83.10  E-value=3.8  Score=30.09  Aligned_cols=44  Identities=9%  Similarity=0.164  Sum_probs=24.1

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          131 KLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       131 ~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      .|+.....|+.++.....-+.+|.+.......+|++|+.+|+.+
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            44445555555555555555555555555555555555555554

>2zvf_A Alanyl-tRNA synthetase; C-terminal, oligomerization domain, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase, nucleotide-binding; 3.20A {Archaeoglobus fulgidus}

Probab=83.06  E-value=3  Score=33.31  Aligned_cols=48  Identities=19%  Similarity=0.259  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHHHHHHh----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          118 AVQMMEQLRTEAQKLKQSN----ENLQEKIKELKAEKNELRDEKQRLKADKE  165 (235)
Q Consensus       118 AIeYIk~Lq~qv~~L~~e~----~~L~~ei~eLk~EknELr~E~~~Lk~e~e  165 (235)
                      |++|+++.+..+.++...+    ..+.+.++.|..+..+|+.|...|+.++-
T Consensus         5 A~~~~~~~~~~l~~~a~~Lk~~~~~l~~~v~~l~~e~k~l~ke~~~l~~~~a   56 (171)
T 2zvf_A            5 AIEAVEEMERLLREASSILRVEPAKLPKTVERFFEEWKDQRKEIERLKSVIA   56 (171)
T ss_dssp             GTHHHHHHHHHHHHHHHTTTCCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555555444322    34445555555555555555554444433

>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=82.85  E-value=1  Score=44.00  Aligned_cols=80  Identities=20%  Similarity=0.281  Sum_probs=35.2

Q ss_pred             HHHHHHHHHhcCCCCCCCCCchh--hHHHHHHHHHHHHHHHHHHHHH---Hh-HHHHHHHHHHHHHHHH-------HHHH
Q 026646           90 LNERFLELGSMLEPGRPPKTDKA--TILSDAVQMMEQLRTEAQKLKQ---SN-ENLQEKIKELKAEKNE-------LRDE  156 (235)
Q Consensus        90 INd~F~eLrslLP~~~~~K~dKa--sIL~dAIeYIk~Lq~qv~~L~~---e~-~~L~~ei~eLk~EknE-------Lr~E  156 (235)
                      +..++.+|+..|...  .|..|-  +......+||++=+.+...++.   ++ +.|+..|.+|+.+++.       ||.-
T Consensus        62 ltkrINELKnqLEdl--sKnsKdseqy~k~~~E~Lr~rq~q~~dNdNtynE~S~ELRRrIqyLKekVdnQlsnIrvLQsn  139 (562)
T 3ghg_A           62 FTNRINKLKNSLFEY--QKNNKDSHSLTTNIMEILRGDFSSANNRDNTYNRVSEDLRSRIEVLKRKVIEKVQHIQLLQKN  139 (562)
T ss_dssp             HHHHHHHHHHHHTHH--HHHHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH--HhhchhHHHHHHHHHHHHHHHHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445566677666543  222221  1233344444332333322222   22 2555666666665553       3333


Q ss_pred             HHHHHHHHHHHHHHH
Q 026646          157 KQRLKADKEKLEQQV  171 (235)
Q Consensus       157 ~~~Lk~e~e~le~ql  171 (235)
                      +..+..+|.|||..|
T Consensus       140 Ledq~~kIQRLEvDI  154 (562)
T 3ghg_A          140 VRAQLVDMKRLEVDI  154 (562)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            444444444554443

>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=82.82  E-value=3.5  Score=30.22  Aligned_cols=24  Identities=21%  Similarity=0.142  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          148 AEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       148 ~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      ..+.+|..+......+|..|+.+|
T Consensus        40 ~~I~eLEk~L~ekd~eI~~LqseL   63 (72)
T 3nmd_A           40 ALIDELELELDQKDELIQMLQNEL   63 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444444444444

>1jcd_A Major outer membrane lipoprotein; protein folding, coiled coil, helix capping, alanine-zipper, membrane protein; 1.30A {Escherichia coli} SCOP: h.1.16.1 PDB: 1eq7_A 1t8z_A* 2guv_A 2gus_A 1jcc_A 1kfn_A 1kfm_A

Probab=82.63  E-value=5.6  Score=27.35  Aligned_cols=44  Identities=11%  Similarity=0.272  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKE  165 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e  165 (235)
                      |.+|-.+|+.|.....+|..++..|+.+...-.+|-.+-...++
T Consensus         6 i~~Lss~V~~L~~kVdqLssdV~al~~~v~~ak~eA~RAN~RlD   49 (52)
T 1jcd_A            6 ADQASSDAQTANAKADQASNDANAARSDAQAAKDDAARANQRAD   49 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            56788888888888888888888888887777777666655544

>1gmj_A ATPase inhibitor; coiled-coil structure, P dependent oligomerization, ATP hydrolysis; 2.2A {Bos taurus} SCOP: h.4.8.1 PDB: 1ohh_H* 1hf9_A

Probab=82.60  E-value=7.1  Score=29.41  Aligned_cols=31  Identities=26%  Similarity=0.329  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          138 NLQEKIKELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       138 ~L~~ei~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      .|.++|..-+.++.+|.++..+.+..|..|.
T Consensus        48 kl~~el~~h~~ei~~le~~i~rhk~~i~~l~   78 (84)
T 1gmj_A           48 HKENEISHHAKEIERLQKEIERHKQSIKKLK   78 (84)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3344444444444444444444444444443

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

Probab=82.58  E-value=12  Score=27.94  Aligned_cols=40  Identities=20%  Similarity=0.463  Sum_probs=18.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          127 TEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       127 ~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      .++.+.+..|..++.++++...       .|..|..++++++.+++.
T Consensus        31 EELs~vr~~ni~~eskL~eae~-------rn~eL~~e~~~l~~~~ee   70 (81)
T 1wt6_A           31 REMEAIRTDNQNFASQLREAEA-------RNRDLEAHVRQLQERMEL   70 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444433       444555555555555554

>3swk_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural; 1.70A {Homo sapiens}

Probab=82.55  E-value=6.3  Score=29.25  Aligned_cols=31  Identities=10%  Similarity=0.272  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          143 IKELKAEKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       143 i~eLk~EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      +..|+....++-=-+..|.++++.|..+|.-
T Consensus        51 ~~~LrkdvD~a~l~r~dLE~kvesL~eEl~f   81 (86)
T 3swk_A           51 LQSFRQDVDNASLARLDLERKVESLQEEIAF   81 (86)
T ss_dssp             HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444433445566666666666543

>3a7o_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.50A {Saccharomyces cerevisiae}

Probab=82.36  E-value=8.1  Score=28.42  Aligned_cols=54  Identities=20%  Similarity=0.242  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          121 MMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       121 YIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      .|+.||.+...-+.+...|++.++--.+....|-||.-.|.-|..-|++.|..+
T Consensus        19 ~l~~Lr~eL~~Ke~eI~~L~e~i~lk~kd~ErLNDEiislNIENNlL~~rl~~l   72 (75)
T 3a7o_A           19 TLAILQKELKSKEQEIRRLKEVIALKNKNTERLNDELISGTIENNVLQQKLSDL   72 (75)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHhhHHHHHhHHHHHHHHHHHHHH
Confidence            566777777777777778777766555566678888888888888888877544

>1uix_A RHO-associated kinase; coiled-coil, transferase; HET: MSE; 1.80A {Bos taurus} SCOP: h.1.27.1

Probab=82.21  E-value=8.1  Score=28.22  Aligned_cols=48  Identities=27%  Similarity=0.399  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          125 LRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       125 Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      |+..+..|..+++.|..+++.+..+...+++|-....+.+.+++.+|+
T Consensus         2 ~~k~v~~l~~E~eel~~klk~~~ee~~~~~eee~~~~~~k~~lek~L~   49 (71)
T 1uix_A            2 STSDVANLANEKEELNNKLKEAQEQLSRLKDEEISAAAIKAQFEKQLL   49 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555566666666666655555555555544444344444444443

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

Probab=82.08  E-value=7.3  Score=33.54  Aligned_cols=53  Identities=17%  Similarity=0.220  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHh
Q 026646          121 MMEQLRTEAQKLKQSNENLQEKIKELKA---------EKNELRDEKQRLKADKEKLEQQVKA  173 (235)
Q Consensus       121 YIk~Lq~qv~~L~~e~~~L~~ei~eLk~---------EknELr~E~~~Lk~e~e~le~qlk~  173 (235)
                      -+..++.++.+++.+...++..++..+.         |++.|..|...++.++..++.++..
T Consensus        54 ~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l~~v~~~kE~~aL~kEie~~~~~i~~lE~eile  115 (256)
T 3na7_A           54 EKLALKLQVSKNEQTLQDTNAKIASIQKKMSEIKSERELRSLNIEEDIAKERSNQANREIEN  115 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444433         2334445556666666666666555

>1x8y_A Lamin A/C; structural protein, intermediate filament protein; 2.20A {Homo sapiens} SCOP: h.1.20.1 PDB: 3v5b_A 3v4w_A 3v4q_A

Probab=82.03  E-value=9.3  Score=28.18  Aligned_cols=50  Identities=14%  Similarity=0.173  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV  171 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~ql  171 (235)
                      +.+++..+..|+.+..+++.++.....|+.+|-+=|..|..||.--..-|
T Consensus        30 l~~~q~~i~~lE~el~~~r~e~~~ql~EYq~LlnvK~~Le~EIatYRkLL   79 (86)
T 1x8y_A           30 RDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLL   79 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            44556667777777777777777777788888888888888776554444

>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=81.57  E-value=4.2  Score=26.16  Aligned_cols=27  Identities=30%  Similarity=0.469  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKA  148 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~  148 (235)
                      +++|...|++|..++..|+.++..|+.
T Consensus         3 MnQLE~KVEeLl~~~~~Le~eV~RLk~   29 (36)
T 1kd8_B            3 VKQLKAKVEELKSKLWHLKNKVARLKK   29 (36)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            456666666666666666666655543

>1uo4_A General control protein GCN4; four helix bundle, cavity, iodobenzene; 1.70A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 1uo3_A 1unt_A 1uo5_A 1unu_A 1unv_A 1uo1_A 2ccf_A 2cce_A 1unx_A 1unw_A 1w5j_A* 1w5k_A* 1u9f_A* 3f86_A* 3f87_A* 3hez_A* 3c3f_A*

Probab=81.56  E-value=2.3  Score=27.09  Aligned_cols=23  Identities=22%  Similarity=0.407  Sum_probs=10.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 026646          139 LQEKIKELKAEKNELRDEKQRLK  161 (235)
Q Consensus       139 L~~ei~eLk~EknELr~E~~~Lk  161 (235)
                      |+.++++|-.++.+|.+|..+||
T Consensus         6 LEdKVEeLl~~n~~Le~EV~RLk   28 (34)
T 1uo4_A            6 IEDKGEEILSKLYHIENELARIK   28 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHH
Confidence            44444444444444554444443

>2bni_A General control protein GCN4; four helix bundle, antiparallel four helix bundle acyl transferase; HET: TYZ; 1.5A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 2ccn_A 1w5k_A* 2ccf_A 2cce_A 1w5j_A* 1uo2_A 1gcl_A 1uo1_A 1unv_A 1uo0_A 1unt_A 1uo5_A 1unz_A 1unx_A 1unu_A 1unw_A 1uo4_A 1uo3_A 1uny_A 1u9f_A* ...

Probab=81.33  E-value=2.3  Score=27.03  Aligned_cols=24  Identities=21%  Similarity=0.515  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          138 NLQEKIKELKAEKNELRDEKQRLK  161 (235)
Q Consensus       138 ~L~~ei~eLk~EknELr~E~~~Lk  161 (235)
                      +|..++++|-.++.+|.+|..+||
T Consensus         5 QLEdKvEeLl~~~~~L~~EV~RLk   28 (34)
T 2bni_A            5 QIEDKLEEILSKGHHICNELARIK   28 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccHHHHHHHHHHH
Confidence            445555555555555555555554

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=81.03  E-value=9  Score=29.84  Aligned_cols=52  Identities=21%  Similarity=0.228  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026646          124 QLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS  175 (235)
Q Consensus       124 ~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk~~~  175 (235)
                      .|.-+|+-|+...+.+.+...+++.+..|...+...+|..+..|+.++..+.
T Consensus        27 al~YqVdlLKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~~lk   78 (103)
T 4h22_A           27 NFMYQVDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEVK   78 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3555888888888888888899999988888889999999999999987753

>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=80.64  E-value=1.9  Score=27.27  Aligned_cols=24  Identities=25%  Similarity=0.401  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          146 LKAEKNELRDEKQRLKADKEKLEQ  169 (235)
Q Consensus       146 Lk~EknELr~E~~~Lk~e~e~le~  169 (235)
                      |.....+|..+|+.|.+|++||..
T Consensus         5 LE~kVEeLl~~n~~Le~EV~RLk~   28 (33)
T 3m48_A            5 LEAKVEELLSKNWNLENEVARLKK   28 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHH
Confidence            334444444444444444444443

>3vmx_A Voltage-gated hydrogen channel 1; coiled-coil, ION channel, ION transport, membrane protein; 1.45A {Mus musculus}

Probab=80.50  E-value=6.9  Score=26.63  Aligned_cols=17  Identities=18%  Similarity=0.194  Sum_probs=6.2

Q ss_pred             HHHHHHHHHHHHHhHHH
Q 026646          123 EQLRTEAQKLKQSNENL  139 (235)
Q Consensus       123 k~Lq~qv~~L~~e~~~L  139 (235)
                      .+|++-...|-.....|
T Consensus         7 ~kLKe~n~~L~~kv~~L   23 (48)
T 3vmx_A            7 LRLKQINIQLATKIQHL   23 (48)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            33333333333333333

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

Probab=80.47  E-value=15  Score=28.75  Aligned_cols=39  Identities=15%  Similarity=0.375  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 026646          116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNELR  154 (235)
Q Consensus       116 ~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr  154 (235)
                      .++..-+..||.++..|...++.|+..|++|.+...+|.
T Consensus        31 ~e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDLE   69 (111)
T 2v66_B           31 AQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLE   69 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHH
Confidence            344455666666666666666666666666666655553

>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=80.23  E-value=16  Score=29.10  Aligned_cols=30  Identities=27%  Similarity=0.415  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          143 IKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       143 i~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      +++|+-|+..|..+.....+++|+|..+..
T Consensus        73 vqeLqgEI~~Lnq~Lq~a~ae~erlr~~~~  102 (121)
T 3mq7_A           73 VEELEGEITTLNHKLQDASAEVERLRRENQ  102 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhch
Confidence            444444444444444444444444444433

>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=80.23  E-value=4.2  Score=37.18  Aligned_cols=52  Identities=17%  Similarity=0.176  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          121 MMEQLRTEAQKLKQSNENLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       121 YIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      =++.|+.++.+|+.......++|+.|+.....++...+.|+.++..|+..+.
T Consensus         6 ~~~~~~~~~~~~e~~i~~~~~~i~~L~~~l~~~~~~i~~l~~~i~~l~~~~~   57 (323)
T 1lwu_C            6 TVQKILEEVRILEQIGVSHDAQIQELSEMWRVNQQFVTRLQQQLVDIRQTCS   57 (323)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3455666666666665555666666666666666555666555555555443

>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=80.21  E-value=3.4  Score=26.58  Aligned_cols=29  Identities=21%  Similarity=0.419  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 026646          122 MEQLRTEAQKLKQSNENLQEKIKELKAEK  150 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei~eLk~Ek  150 (235)
                      +++|..+|++|..++..|+.++..|+...
T Consensus         3 MnQLE~kVEeLl~~~~~Le~EV~RL~~ll   31 (36)
T 1kd8_A            3 VKQLEAEVEEIESEVWHLENEVARLEKEN   31 (36)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence            45666667766666666666666655433

>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=80.07  E-value=3.8  Score=25.39  Aligned_cols=25  Identities=32%  Similarity=0.348  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          144 KELKAEKNELRDEKQRLKADKEKLE  168 (235)
Q Consensus       144 ~eLk~EknELr~E~~~Lk~e~e~le  168 (235)
                      ..|++|+.-|..|...||-||--|.
T Consensus         5 aalkqeiaalkkeiaalkfeiaalk   29 (33)
T 4dzn_A            5 AALKQEIAALKKEIAALKFEIAALK   29 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444443

---

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	235
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	1e-19
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	4e-16
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	4e-15
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-14
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	4e-14
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	8e-10
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	1e-08
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	6e-07

>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 = 78.0 bits (192), Expect = 1e-19
 Identities = 16/73 (21%), Positives = 34/73 (46%)

Query: 82  REKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQE 141
            E+ RRD + + F  L   +   +  K  +A IL  A + ++ +R +    +Q  ++L+ 
Sbjct: 9   LERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR 68

Query: 142 KIKELKAEKNELR 154
           +   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 = 69.2 bits (169), Expect = 4e-16
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 82  REKLRRDRLNERFLELGSML-EPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQ 140
            E+ RR+ L   F  L   + E     K  K  IL  A   +  ++ E QKL    + L+
Sbjct: 13  LERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR 72

Query: 141 EKIKELKAEKNELR 154
           ++ ++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 = 66.1 bits (161), Expect = 4e-15
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 82  REKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQE 141
            EK  R  +N++ +EL   L  G   K +K+ +L  A+  +  L+   QKLKQ N +L+ 
Sbjct: 13  IEKRYRSSINDKIIELKD-LVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT 71

Query: 142 KIKELKAEK 150
            + + 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 = 64.5 bits (157), Expect = 1e-14
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 82  REKLRRDRLNERFLELGSMLEPGRP-PKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQ 140
            EK RR  L     +L  ++  G    +    ++L+ A   +++L    +K     + LQ
Sbjct: 8   MEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ 67

Query: 141 EKIKELKAEKNE 152
            + + 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 = 62.8 bits (153), Expect = 4e-14
 Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 87  RDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKEL 146
           R  +N++ +EL  ++  G   K  K+ +L  A+  ++ L+    KL+Q N  L+   ++ 
Sbjct: 1   RSSINDKIIELKDLV-MGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQKN 59

Query: 147 K 147
           K
Sbjct: 60  K 60

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (123), Expect = 8e-10
 Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 82  REKLRRDRLNERFLELGSML----EPGRPPKTDKATILSDAVQMMEQLRTEAQK 131
            E+ RRD++N   ++L  ++             K  ILS A   +++LR    +
Sbjct: 12  VERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR 65

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 68

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.3 bits (115), Expect = 1e-08
 Identities = 13/45 (28%), Positives = 22/45 (48%)

Query: 82  REKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLR 126
           RE+ R  ++NE F  L          +  K  IL +A++ +E L+
Sbjct: 19  RERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQ 63

>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 = 43.3 bits (102), Expect = 6e-07
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 5/54 (9%)

Query: 82  REKLRRDRLNERFLELGSML-----EPGRPPKTDKATILSDAVQMMEQLRTEAQ 130
            E+ RR+RL     EL S++     +        KAT +  A + +  L+    
Sbjct: 9   AEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	235
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.75
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.73
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.72
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.57
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.56
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.55
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.47
d1lrza1	65	Methicillin resistance protein FemA probable tRNA-	88.66
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	85.43
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	85.01
d1fxka_	107	Prefoldin beta subunit {Archaeon Methanobacterium	82.59

>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=99.75  E-value=1.2e-18  Score=128.83  Aligned_cols=79  Identities=20%  Similarity=0.322  Sum_probs=68.4

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNEL  153 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknEL  153 (235)
                      ++.+|+.+||+||++||+.|.+|+++||.....|++|++||..||+||++|+.+++.|..+.+.|+.+...|..+.+.|
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~L   80 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRAL   80 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3568999999999999999999999999765589999999999999999999999998888887777766666655544

>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=99.73  E-value=6.4e-18  Score=123.71  Aligned_cols=75  Identities=20%  Similarity=0.279  Sum_probs=66.4

Q ss_pred             cCcchHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 026646           76 SGSKACREKLRRDRLNERFLELGSMLEPGR-PPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEK  150 (235)
Q Consensus        76 ~~sH~~~ERrRRekINd~F~eLrslLP~~~-~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~Ek  150 (235)
                      +.+|+.+||+||++||+.|.+|+++||++. ..|.+|++||..||+||+.|+.+++.|..+.+.|..+...|+.+.
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~~~~~L~~~l   77 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQL   77 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            457999999999999999999999999753 368999999999999999999999999988888887777776543

>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=99.72  E-value=6.7e-18  Score=125.88  Aligned_cols=80  Identities=24%  Similarity=0.337  Sum_probs=69.0

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGR-PPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAEKNEL  153 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~-~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~EknEL  153 (235)
                      ++.+|+.+||+||++||+.|..|+++||+.. ..|.+|++||..||+||+.|+.+++.|..+.+.|..+...|..+.+.|
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            4568999999999999999999999999743 368999999999999999999999999888888877777776666555


Q ss_pred             H
Q 026646          154 R  154 (235)
Q Consensus       154 r  154 (235)
                      +
T Consensus        86 ~   86 (88)
T d1nkpa_          86 G   86 (88)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.72  E-value=8.7e-18  Score=123.70  Aligned_cols=72  Identities=26%  Similarity=0.393  Sum_probs=64.7

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKIKELK  147 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk  147 (235)
                      .+.+|+.+||+||++||+.|.+|+++||... .|++|++||.+||+||++|+.+++.|+.++..|+..++.++
T Consensus         6 kR~~H~~~Er~RR~~in~~~~~L~~llP~~~-~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~~~~~~   77 (80)
T d1am9a_           6 KRTAHNAIEKRYRSSINDKIIELKDLVVGTE-AKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTCSS-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            4568999999999999999999999999753 79999999999999999999999999999888877765543

>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=99.57  E-value=4.3e-16  Score=111.83  Aligned_cols=58  Identities=22%  Similarity=0.289  Sum_probs=52.6

Q ss_pred             ccCcCcchHHHHHHHHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHH
Q 026646           73 CCVSGSKACREKLRRDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQ  130 (235)
Q Consensus        73 ~~~~~sH~~~ERrRRekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~  130 (235)
                      ..++.+|+.+||+||++||+.|..|+++||.+...|++|++||..||+||++|++.++
T Consensus        10 ~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          10 ADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            3467889999999999999999999999998766799999999999999999997654

>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=99.56  E-value=1e-15  Score=108.05  Aligned_cols=55  Identities=25%  Similarity=0.354  Sum_probs=49.3

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCC-----CCCCCCchhhHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEP-----GRPPKTDKATILSDAVQMMEQLRTEA  129 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~-----~~~~K~dKasIL~dAIeYIk~Lq~qv  129 (235)
                      ++.+|+.+||+||++||+.|.+|+++||+     +...|++|++||..||+||++|++++
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            35689999999999999999999999994     23479999999999999999999764

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.8e-15  Score=106.32  Aligned_cols=56  Identities=25%  Similarity=0.393  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHHHhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 026646           87 RDRLNERFLELGSMLEPGRPPKTDKATILSDAVQMMEQLRTEAQKLKQSNENLQEKI  143 (235)
Q Consensus        87 RekINd~F~eLrslLP~~~~~K~dKasIL~dAIeYIk~Lq~qv~~L~~e~~~L~~ei  143 (235)
                      |++||++|.+|+++||.+. .|+|||+||.+||+||+.|+.+++.|++++..|+...
T Consensus         1 R~~in~~f~~L~~lvP~~~-~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~   56 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTD-AKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLAN   56 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSS-CCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCC-CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999999764 6999999999999999999999999999998887654

>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=99.47  E-value=5.2e-15  Score=104.95  Aligned_cols=55  Identities=24%  Similarity=0.383  Sum_probs=49.2

Q ss_pred             CcCcchHHHHHHHHHHHHHHHHHHhcCCCCC----CCCCchhhHHHHHHHHHHHHHHHH
Q 026646           75 VSGSKACREKLRRDRLNERFLELGSMLEPGR----PPKTDKATILSDAVQMMEQLRTEA  129 (235)
Q Consensus        75 ~~~sH~~~ERrRRekINd~F~eLrslLP~~~----~~K~dKasIL~dAIeYIk~Lq~qv  129 (235)
                      ++.+|+.+||+||++||+.|.+|+++||.+.    ..|.+|++||..||+||++|+++.
T Consensus         5 rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            4567999999999999999999999999742    369999999999999999998764

>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=88.66  E-value=1.9  Score=29.17  Aligned_cols=53  Identities=11%  Similarity=0.214  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026646          120 QMMEQLRTEAQKLKQSNENLQEKIKE------LKAEKNELRDEKQRLKADKEKLEQQVK  172 (235)
Q Consensus       120 eYIk~Lq~qv~~L~~e~~~L~~ei~e------Lk~EknELr~E~~~Lk~e~e~le~qlk  172 (235)
                      +||..|+.+...|...+..+...++.      -+..+.+|.+....+...|+..++.+.
T Consensus         3 eYl~~L~~~~~~L~~~i~k~~~~leknP~skK~~nk~~el~~Q~~s~~~ki~Ea~~li~   61 (65)
T d1lrza1           3 EYIKELNEERDILNKDLNKALKDIEKRPENKKAHNKRDNLQQQLDANEQKIEEGKRLQE   61 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            79999999999999999888877633      444556666666666666666655544

>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=85.43  E-value=4.7  Score=28.59  Aligned_cols=53  Identities=19%  Similarity=0.410  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          122 MEQLRTEAQKLKQSNENLQEKI--------KELKAEKNELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       122 Ik~Lq~qv~~L~~e~~~L~~ei--------~eLk~EknELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      .++|+.+++.|+.+...+..+|        .+|..+..+|.++...|..+...++.++..+
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            3444555555555444443333        4445555555555555555666666666554

>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=85.01  E-value=2.9  Score=29.74  Aligned_cols=56  Identities=18%  Similarity=0.305  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHhc
Q 026646          119 VQMMEQLRTEAQKLKQSNENLQEKIKELKAEK--------NELRDEKQRLKADKEKLEQQVKAM  174 (235)
Q Consensus       119 IeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~Ek--------nELr~E~~~Lk~e~e~le~qlk~~  174 (235)
                      ++.|-.|-.+...+..+.+.|+.+.+.+..+.        .+|..+...|+.++..++.+++.+
T Consensus        27 ld~i~~ld~~rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~   90 (110)
T d1seta1          27 LEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREK   90 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45566677777788888888887777776554        334445556667777777776654

>d1fxka_ a.2.5.1 (A:) Prefoldin beta subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Prefoldin
family: Prefoldin
domain: Prefoldin beta subunit
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=82.59  E-value=6  Score=28.00  Aligned_cols=34  Identities=18%  Similarity=0.342  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 026646          116 SDAVQMMEQLRTEAQKLKQSNENLQEKIKELKAE  149 (235)
Q Consensus       116 ~dAIeYIk~Lq~qv~~L~~e~~~L~~ei~eLk~E  149 (235)
                      ...+.-+..|+++.+.+.....+|..++++...-
T Consensus         4 qe~~~~~q~lq~el~~~~~q~~~le~q~~E~~~v   37 (107)
T d1fxka_           4 QHQLAQFQQLQQQAQAISVQKQTVEMQINETQKA   37 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455566666766666666666665554444433