Citrus Sinensis ID: 026702

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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
MSSPYNSNWIFDCGLLDDIGVSGGDLPSLDPPEVLWSSSTSNPPLSAEFNDSFGNLDAFKETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEcccHcccccccccccccccccccccccccccccccEEcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccc
Coil and Loop (DISEMBL)
msspynsnwifdcgllddigvsggdlpsldppevlwssstsnpplsaefndsfgnldafketgsrkrvrsgscsasgskACREKMRRDRLNDRFMELAsildpgrppkmdkTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALssqpaflphpppvpapfsapgqvvggklvplvgypgvsmwqfmppaavdtsqdhvlrppva
Flexible Loop (DISEMBL)
msspynsnWIFDCGLLDDIGVSGGDLPSLDPPEVLWSSSTSNPPLSAEFNDSFGNLDAFketgsrkrvrsgscsasgskacrekMRRDRLNDRFMElasildpgrppkmDKTVLLADAVQMVTQLRDEAQklkvsnekllgkinelkceknelrdEKQRLKNEKENLERQVKALSSQPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA
Low Complexity Region (SEG)
MSSPYNSNWIFDCGLLDDIGVSGGDLPSLDPPEVLWSSSTSNPPLSAEFNDSFGNLDAFKETGSRKRVrsgscsasgskacrEKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQpaflphpppvpapfsapGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA
Disordered region (IsUnstruct)
******SNWIFDCGLLDDIGVSGG****************************************************************************************VLLADAVQMVTQ***********************************************************************QVVGGKLVPLVGYPGVSMWQFMPP****************
Disordered Region (DISOPRED)
***PYNSNWIFDCGLLDDIGVSGGD*****************************************************************NDRFMELASIL********DKTVLLADAVQMVTQLR********************************************************************************GYPGVSMW****************RPP**
Disordered Region (DISEMBL)
MSSPYNSNWIFDCGLLDDIGVSGGDLPSLDPPEVLWSSSTSNPPLSAEFNDSFGNLDAFKE***********************MRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA
Disordered Region (DISPRO)
*****NSNWIFDCGLLDDIGVSGGDLPSLDPP**********************************************K*CREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPP**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooo
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)
MSSPYNSNWIFDCGLLDDIGVSGGDLPSLDPPEVLWSSSTSNPPLSAEFNDSFGNLDAFKETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA
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	0.982	0.987	0.613	6e-70
Q9C682	226	Transcription factor bHLH	no	no	0.944	0.982	0.531	4e-61
Q8L467	283	Transcription factor bHLH	no	no	0.693	0.575	0.505	3e-41
Q9LTC7	320	Transcription factor bHLH	no	no	0.740	0.543	0.491	6e-39
Q9LT23	337	Transcription factor bHLH	no	no	0.625	0.436	0.343	1e-15
Q8W2F2	286	Transcription factor bHLH	no	no	0.523	0.430	0.387	2e-13
Q9SN74	240	Transcription factor bHLH	no	no	0.655	0.641	0.275	2e-07
Q9LUK7	511	Transcription factor bHLH	no	no	0.268	0.123	0.384	3e-05
O49687	589	Transcription factor MYC4	no	no	0.310	0.123	0.341	0.0005
Q9FIP9	592	Transcription factor ATR2	no	no	0.340	0.135	0.317	0.0009

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

 Score =  263 bits (673), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 146/238 (61%), Positives = 170/238 (71%), Gaps = 7/238 (2%)

Query: 1   MSSPYNSNWIFDCGLLD-DIGVSGGDLPSLDPPEVLWSSSTSNPPLSAEFNDSFGNLDAF 59
           M SP N+NWI  C L+D D G      P    P       +SN   SA  + S GN +A 
Sbjct: 1   MVSPENANWI--CDLIDADYGSFTIQGPGFSWPVQQPIGVSSNS--SAGVDGSAGNSEAS 56

Query: 60  KETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAV 119
           KE GS+KR R  S SA+ SKACREK RRDRLND+FMEL +IL+PG PPK DK  +L DAV
Sbjct: 57  KEPGSKKRGRCESSSATSSKACREKQRRDRLNDKFMELGAILEPGNPPKTDKAAILVDAV 116

Query: 120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSS-QP 178
           +MVTQLR EAQKLK SN  L  KI ELK EKNELRDEKQRLK EKE LE+Q+KA+++ QP
Sbjct: 117 RMVTQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQRLKTEKEKLEQQLKAMNAPQP 176

Query: 179 AFLPHPPPVPAPF-SAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
           +F P PP +P  F SA GQ  G K+VP++ YPGV+MWQFMPPA+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 =  234 bits (597), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 127/239 (53%), Positives = 160/239 (66%), Gaps = 17/239 (7%)

Query: 1   MSSPYNSNWIFDCGLLDDIGVSGGDLPSLDPPEVLWSSSTSNPPLSAEFNDSFGNLDAFK 60
           M SP N+NW+ D  L++  G      P+   P  +  S+T    +S E +    + D  K
Sbjct: 1   MVSPENTNWLSDYPLIE--GAFSDQNPTF--PWQIDGSAT----VSVEVDGFLCDADVIK 52

Query: 61  ETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQ 120
           E  SRKR+++ SC+ S SKACREK RRDRLND+F EL+S+L+PGR PK DK  ++ DA++
Sbjct: 53  EPSSRKRIKTESCTGSNSKACREKQRRDRLNDKFTELSSVLEPGRTPKTDKVAIINDAIR 112

Query: 121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSS---- 176
           MV Q RDEAQKLK  N  L  KI ELK EKNELRDEKQ+LK EKE +++Q+KA+ +    
Sbjct: 113 MVNQARDEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQPQP 172

Query: 177 QPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
           QP FLP+P  +     +  Q  G KLVP   YPG +MWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 173 QPCFLPNPQTL-----SQAQAPGSKLVPFTTYPGFAMWQFMPPAAVDTSQDHVLRPPVA 226

Arabidopsis thaliana (taxid: 3702)

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

 Score =  168 bits (426), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 88/174 (50%), Positives = 123/174 (70%), Gaps = 11/174 (6%)

Query: 64  SRKRVRSGSCS-ASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMV 122
           SRKR R+GSCS   G+KACRE++RR++LN+RFM+L+S+L+PGR PK DK  +L DA++++
Sbjct: 119 SRKRARTGSCSRGGGTKACRERLRREKLNERFMDLSSVLEPGRTPKTDKPAILDDAIRIL 178

Query: 123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSS-QPAFL 181
            QLRDEA KL+ +N+KLL +I  LK EKNELR+EK  LK +KE  E+Q+K++++    F+
Sbjct: 179 NQLRDEALKLEETNQKLLEEIKSLKAEKNELREEKLVLKADKEKTEQQLKSMTAPSSGFI 238

Query: 182 PHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
           PH   +PA F+     V     P  GY  + MW +MP +  DTS+D  LRPP A
Sbjct: 239 PH---IPAAFNHNKMAV----YPSYGY--MPMWHYMPQSVRDTSRDQELRPPAA 283

Arabidopsis thaliana (taxid: 3702)

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

 Score =  160 bits (405), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 89/181 (49%), Positives = 123/181 (67%), Gaps = 7/181 (3%)

Query: 57  DAFKETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLA 116
           + F+E  S KR R+GSCS  G+KACREK+RR++LND+FM+L+S+L+PGR PK DK+ +L 
Sbjct: 145 EEFEEECSGKRRRTGSCSKPGTKACREKLRREKLNDKFMDLSSVLEPGRTPKTDKSAILD 204

Query: 117 DAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSS 176
           DA+++V QLR EA +L+ +N+KLL +I  LK +KNELR+EK  LK EKE +E+Q+K++  
Sbjct: 205 DAIRVVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLVLKAEKEKMEQQLKSMVV 264

Query: 177 -QPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGY-PGVSMWQFMPPAAVDTSQDHVLRPPV 234
             P F+P     PA F +    V     P   Y P + MW  +PPA  DTS+D    PPV
Sbjct: 265 PSPGFMPSQH--PAAFHSHKMAVA---YPYGYYPPNMPMWSPLPPADRDTSRDLKNLPPV 319

Query: 235 A 235
           A
Sbjct: 320 A 320

Arabidopsis thaliana (taxid: 3702)

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

 Score = 83.6 bits (205), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 59/172 (34%), Positives = 88/172 (51%), Gaps = 25/172 (14%)

Query: 79  KACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEK 138
           KA REK+RR++LN+ F+EL ++LDP RP K DK  +L D VQ++ +L  E  KLK     
Sbjct: 63  KAGREKLRREKLNEHFVELGNVLDPERP-KNDKATILTDTVQLLKELTSEVNKLKSEYTA 121

Query: 139 LLGKINELKCEKNELRDEKQRLKNEKENL----ERQVKALSSQPAFLPH----------- 183
           L  +  EL  EKN+LR+EK  LK++ ENL    +++++++S   A + H           
Sbjct: 122 LTDESRELTQEKNDLREEKTSLKSDIENLNLQYQQRLRSMSPWGAAMDHTVMMAPPPSFP 181

Query: 184 --------PPPVPAPFSAPGQVVGGKLVP-LVGYPGVSMWQFMPPAAVDTSQ 226
                   P  +P   S P     G   P ++  P  +   +MPP  V   Q
Sbjct: 182 YPMPIAMPPGSIPMHPSMPSYTYFGNQNPSMIPAPCPTYMPYMPPNTVVEQQ 233

Arabidopsis thaliana (taxid: 3702)

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

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 50/129 (38%), Positives = 74/129 (57%), Gaps = 6/129 (4%)

Query: 69  RSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDE 128
           +   CS    KA REK+RRD+L ++F+EL + LDP RP K DK  +L D +QM+  + ++
Sbjct: 42  KEAVCS---QKAEREKLRRDKLKEQFLELGNALDPNRP-KSDKASVLTDTIQMLKDVMNQ 97

Query: 129 AQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA-LSSQPAFLPHPPPV 187
             +LK   E L  +  EL  EK+ELR+EK  LK++ E L  Q +  + +   ++PH    
Sbjct: 98  VDRLKAEYETLSQESRELIQEKSELREEKATLKSDIEILNAQYQHRIKTMVPWVPH-YSY 156

Query: 188 PAPFSAPGQ 196
             PF A  Q
Sbjct: 157 HIPFVAITQ 165

Arabidopsis thaliana (taxid: 3702)

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

 Score = 56.6 bits (135), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 46/167 (27%), Positives = 80/167 (47%), Gaps = 13/167 (7%)

Query: 66  KRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQL 125
           +R R G      +KA RE+++R+ LN+ F+ELA  L+  +     K  +L +A + +  +
Sbjct: 19  ERCRKGKVPKRINKAVRERLKREHLNELFIELADTLELNQQ-NSGKASILCEATRFLKDV 77

Query: 126 RDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAFLPHPP 185
             + + L+  +  LL + + +  EKNEL++E   L+ E   L+ +++A ++Q    P   
Sbjct: 78  FGQIESLRKEHASLLSESSYVTTEKNELKEETSVLETEISKLQNEIEARANQSK--PDLN 135

Query: 186 PVPAP--------FSAPGQVVGGKLVPLVGYPGV--SMWQFMPPAAV 222
             PAP           P +V     +P+   PG   S     PPA V
Sbjct: 136 TSPAPEYHHHHYQQQHPERVSQFPGLPIFQGPGFQQSATTLHPPATV 182

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LUK7|BH028_ARATH Transcription factor bHLH28 OS=Arabidopsis thaliana GN=BHLH28 PE=2 SV=1

 Score = 48.9 bits (115), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 41/65 (63%), Gaps = 2/65 (3%)

Query: 83  EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
           E+MRR++LN RF  L +++      KMDKT LL DAV  + +L+ +A+ +++    +  +
Sbjct: 348 ERMRREKLNHRFYALRAVVP--NVSKMDKTSLLEDAVCYINELKSKAENVELEKHAIEIQ 405

Query: 143 INELK 147
            NELK
Sbjct: 406 FNELK 410

Arabidopsis thaliana (taxid: 3702)

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

 Score = 44.7 bits (104), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 47/79 (59%), Gaps = 6/79 (7%)

Query: 83  EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
           E+ RR++LN RF  L +++ P    KMDK  LL DA+  +++L+ + QK +   E+L  +
Sbjct: 421 ERQRREKLNQRFYSLRAVV-P-NVSKMDKASLLGDAISYISELKSKLQKAESDKEELQKQ 478

Query: 143 INELKCE----KNELRDEK 157
           I+ +  E    K+ ++D K
Sbjct: 479 IDVMNKEAGNAKSSVKDRK 497

Arabidopsis thaliana (taxid: 3702)

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

 Score = 43.9 bits (102), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 2/82 (2%)

Query: 83  EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
           E+ RR++LN RF  L +++ P    KMDK  LL DA+  + +L+ + Q+ +   E++  K
Sbjct: 420 ERQRREKLNQRFYSLRAVV-P-NVSKMDKASLLGDAISYINELKSKLQQAESDKEEIQKK 477

Query: 143 INELKCEKNELRDEKQRLKNEK 164
           ++ +  E N  +    R K  K
Sbjct: 478 LDGMSKEGNNGKGCGSRAKERK 499

Involved in tryptophan and other stress-responsive gene regulation.

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
224114243	243	predicted protein [Populus trichocarpa]	1.0	0.967	0.711	1e-91
255555061	229	DNA binding protein, putative [Ricinus c	0.970	0.995	0.703	4e-87
359497014	232	PREDICTED: transcription factor ILR3-lik	0.944	0.956	0.708	1e-84
224076706	243	predicted protein [Populus trichocarpa]	1.0	0.967	0.699	8e-82
297741862	225	unnamed protein product [Vitis vinifera]	0.812	0.848	0.774	1e-80
359485584	240	PREDICTED: transcription factor ILR3-lik	1.0	0.979	0.638	3e-80
449454698	235	PREDICTED: transcription factor ILR3-lik	1.0	1.0	0.617	2e-79
357474831	237	Transcription factor ILR3 [Medicago trun	0.974	0.966	0.621	2e-74
225461144	237	PREDICTED: transcription factor ILR3 [Vi	0.982	0.974	0.626	2e-74
297739325	223	unnamed protein product [Vitis vinifera]	0.936	0.986	0.641	4e-74

>gi|224114243|ref|XP_002316706.1| predicted protein [Populus trichocarpa] gi|222859771|gb|EEE97318.1| predicted protein [Populus trichocarpa]

 Score =  342 bits (876), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 173/243 (71%), Positives = 195/243 (80%), Gaps = 8/243 (3%)

Query: 1   MSSPY-NSNWIFDCGLLDDIGVSGGDLPSLD-----PPEVLWSSS--TSNPPLSAEFNDS 52
           M SP  N NW+FDCGL++DI V GGDL  L+     P   LWSS   T +  LS EFN+S
Sbjct: 1   MVSPNENDNWVFDCGLIEDISVPGGDLLGLESLDETPNGSLWSSHNFTDSAFLSVEFNNS 60

Query: 53  FGNLDAFKETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKT 112
           + N D  KE+GSRKRVR GS +A+GSKACREKMRRDRLNDRF EL ++LDPGRPPK+DK+
Sbjct: 61  YENSDGHKESGSRKRVRPGSSNATGSKACREKMRRDRLNDRFTELGALLDPGRPPKVDKS 120

Query: 113 VLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK 172
            +L DA +MVTQLRDE+QKLK SN  L  KI+ELK EKNELRDEKQRLK EKENLERQVK
Sbjct: 121 AILVDAARMVTQLRDESQKLKESNVSLQEKIDELKAEKNELRDEKQRLKTEKENLERQVK 180

Query: 173 ALSSQPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRP 232
           ALS+ P FLPHP  +PAPFSAPGQVVG KL+P VGYPG+SMWQFMPPA VDTSQDHVLRP
Sbjct: 181 ALSTPPNFLPHPSAIPAPFSAPGQVVGSKLMPFVGYPGISMWQFMPPAVVDTSQDHVLRP 240

Query: 233 PVA 235
           PVA
Sbjct: 241 PVA 243

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555061|ref|XP_002518568.1| DNA binding protein, putative [Ricinus communis] gi|223542413|gb|EEF43955.1| DNA binding protein, putative [Ricinus communis]

 Score =  326 bits (836), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 166/236 (70%), Positives = 188/236 (79%), Gaps = 8/236 (3%)

Query: 1   MSSPY-NSNWIFDCGLLDDIGVSGGDLPSLDPPEVLWSSSTSNPPLSAEFNDSFGNLDAF 59
           M SP  N+NW FD GL++DI V GGDLPSLDP   LWSS    P LS EF+DS G+    
Sbjct: 1   MVSPSDNANWAFDYGLIEDIPVPGGDLPSLDP---LWSS----PSLSVEFDDSLGSSQCL 53

Query: 60  KETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAV 119
           ++ GSRKRVR GSCS  GSKACREKMRRD+LNDRFMEL ++LDPGRPPKMDK+V+LADA+
Sbjct: 54  RDNGSRKRVRPGSCSGLGSKACREKMRRDKLNDRFMELGALLDPGRPPKMDKSVILADAM 113

Query: 120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPA 179
           +MV QLR EAQKLK SNE L  K+NELK EKNELRDEKQRLK EKE++ERQV ALS+   
Sbjct: 114 KMVNQLRAEAQKLKESNENLQEKVNELKVEKNELRDEKQRLKTEKESIERQVNALSASAR 173

Query: 180 FLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
           FLPH P +PAPFS+P QV+G KLVP+VGYPGV MWQ MPPA VDTSQD VLR P A
Sbjct: 174 FLPHLPAIPAPFSSPSQVIGSKLVPIVGYPGVPMWQLMPPATVDTSQDPVLRSPAA 229

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  318 bits (814), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 163/230 (70%), Positives = 184/230 (80%), Gaps = 8/230 (3%)

Query: 8   NWIFDCGLLDDIGVSGGDLPSLDPPEVLWSSS--TSNPPLSAEFNDSFGNLDAFKETGSR 65
           NWIFD GL+DD+ V     PSL      W S   T++  L  EF+DS  NLD  KE  SR
Sbjct: 9   NWIFDYGLIDDVPV-----PSLQA-TFNWPSHDFTASAALGVEFDDSPVNLDDVKENHSR 62

Query: 66  KRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQL 125
           KR+RSG CSASGSKACREK+RRDRLNDRF+EL SIL+PGRPPKMDK V+L+DA++M+TQL
Sbjct: 63  KRMRSGLCSASGSKACREKVRRDRLNDRFLELGSILEPGRPPKMDKAVILSDALRMMTQL 122

Query: 126 RDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAFLPHPP 185
           R E QKLK S E L  KINELK EKNELRDEKQRLK EKEN+ +Q+KALSSQ  FLPHP 
Sbjct: 123 RSEGQKLKKSCEDLQEKINELKAEKNELRDEKQRLKTEKENIVQQIKALSSQAGFLPHPS 182

Query: 186 PVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
            +PAPF+APGQVVG KL+P +GYPGVSMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 183 AIPAPFAAPGQVVGSKLMPFIGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 232

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224076706|ref|XP_002304984.1| predicted protein [Populus trichocarpa] gi|222847948|gb|EEE85495.1| predicted protein [Populus trichocarpa]

 Score =  309 bits (791), Expect = 8e-82,   Method: Compositional matrix adjust.
 Identities = 170/243 (69%), Positives = 192/243 (79%), Gaps = 8/243 (3%)

Query: 1   MSSPY-NSNWIFDCGLLDDIGVSGGD---LPSLD--PPEVLWSSSTSNPP--LSAEFNDS 52
           M SP  N+NW+FDCGL++D+ V  G+   L SLD  P   LWSS + N    LSAEFN+S
Sbjct: 1   MVSPNDNANWVFDCGLIEDVPVPVGEQLCLESLDETPNGSLWSSHSFNDTAFLSAEFNNS 60

Query: 53  FGNLDAFKETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKT 112
           F N D  KE G RKRVR GS +A GSKACREKMRRDRLNDRFMEL ++LDPGRPPK+DK+
Sbjct: 61  FENSDGLKEIGFRKRVRHGSGNAPGSKACREKMRRDRLNDRFMELGALLDPGRPPKVDKS 120

Query: 113 VLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK 172
            +L DA +MVTQLRDE+QKLK S E L  KI+ELK EKNELRDEKQ+LK EKENLE Q K
Sbjct: 121 AMLVDAARMVTQLRDESQKLKESIESLQEKIDELKAEKNELRDEKQKLKMEKENLEWQQK 180

Query: 173 ALSSQPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRP 232
           ALS  P +LPHPP +PAPFSAPGQVVG KL+P VGYPG+SMWQFMPP  VDTSQDHVLRP
Sbjct: 181 ALSPPPTYLPHPPAIPAPFSAPGQVVGSKLMPFVGYPGISMWQFMPPTVVDTSQDHVLRP 240

Query: 233 PVA 235
           PVA
Sbjct: 241 PVA 243

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741862|emb|CBI33226.3| unnamed protein product [Vitis vinifera]

 Score =  305 bits (780), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 148/191 (77%), Positives = 165/191 (86%)

Query: 45  LSAEFNDSFGNLDAFKETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPG 104
           LS EF+DS  NLD  KE  SRKR+RSG CSASGSKACREK+RRDRLNDRF+EL SIL+PG
Sbjct: 35  LSVEFDDSPVNLDDVKENHSRKRMRSGLCSASGSKACREKVRRDRLNDRFLELGSILEPG 94

Query: 105 RPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEK 164
           RPPKMDK V+L+DA++M+TQLR E QKLK S E L  KINELK EKNELRDEKQRLK EK
Sbjct: 95  RPPKMDKAVILSDALRMMTQLRSEGQKLKKSCEDLQEKINELKAEKNELRDEKQRLKTEK 154

Query: 165 ENLERQVKALSSQPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDT 224
           EN+ +Q+KALSSQ  FLPHP  +PAPF+APGQVVG KL+P +GYPGVSMWQFMPPAAVDT
Sbjct: 155 ENIVQQIKALSSQAGFLPHPSAIPAPFAAPGQVVGSKLMPFIGYPGVSMWQFMPPAAVDT 214

Query: 225 SQDHVLRPPVA 235
           SQDHVLRPPVA
Sbjct: 215 SQDHVLRPPVA 225

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  303 bits (777), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 181/238 (76%), Gaps = 3/238 (1%)

Query: 1   MSSPYNSNWIFDCGLLDDIGVSGGDLPSLDPPEVL-WSSST--SNPPLSAEFNDSFGNLD 57
           + S  NSNW+FD GL++DI V GG+ P   P     W S    S+  +S E + SFG+ D
Sbjct: 3   LDSSENSNWLFDYGLMEDITVPGGEFPEPTPGTGFSWPSQALKSSSSVSLEADCSFGDSD 62

Query: 58  AFKETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLAD 117
             KE G RKR++  SC A+G+KACREK+RRDRLN+RF+EL SIL+PGRPPK DK  +L+D
Sbjct: 63  GLKELGPRKRLKHESCGATGTKACREKLRRDRLNERFLELGSILEPGRPPKTDKAAILSD 122

Query: 118 AVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQ 177
           AV+MVTQLR EAQKLK SN  L  KI ELK EKNELRDEKQRLK EKE LE+QVKA+S+Q
Sbjct: 123 AVRMVTQLRSEAQKLKESNGDLQEKIKELKAEKNELRDEKQRLKAEKEKLEQQVKAISAQ 182

Query: 178 PAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
           P FLPHP  +PA F+A G+  G KL+P +GYP V+MWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 183 PGFLPHPSAMPAAFAAQGRAPGNKLMPFIGYPSVAMWQFMPPAAVDTSQDHVLRPPVA 240

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449454698|ref|XP_004145091.1| PREDICTED: transcription factor ILR3-like [Cucumis sativus] gi|449474426|ref|XP_004154169.1| PREDICTED: transcription factor ILR3-like [Cucumis sativus] gi|449520760|ref|XP_004167401.1| PREDICTED: transcription factor ILR3-like [Cucumis sativus]

 Score =  301 bits (770), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 145/235 (61%), Positives = 183/235 (77%)

Query: 1   MSSPYNSNWIFDCGLLDDIGVSGGDLPSLDPPEVLWSSSTSNPPLSAEFNDSFGNLDAFK 60
           M SP  ++W+FD G++++I V GGDLPSLD P     S         +F++  G  +  K
Sbjct: 1   MGSPELTDWVFDYGVIENIPVPGGDLPSLDLPSFTLPSCDFTASFREDFDEPLGMEEDVK 60

Query: 61  ETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQ 120
           E+ SRKR+ SGS +A  SKA +EK+RRD+LNDRF+EL SIL+ GRPPK+DK+ +L DAV+
Sbjct: 61  ESRSRKRMSSGSSNAFESKARKEKIRRDKLNDRFLELNSILNHGRPPKIDKSAILGDAVR 120

Query: 121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAF 180
           M+ QLRDEAQKLK SNE  L KINE+K EKNELRDEKQRLK  K++LE+++K  ++QP F
Sbjct: 121 MIIQLRDEAQKLKESNESSLEKINEMKAEKNELRDEKQRLKEAKDSLEKKMKGFNTQPTF 180

Query: 181 LPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
           LPHPP +PA FS+P Q+VGGKLVP++GYPGVSMWQFMPP A+DTSQDHVLRPPVA
Sbjct: 181 LPHPPAIPAGFSSPNQIVGGKLVPVIGYPGVSMWQFMPPGAIDTSQDHVLRPPVA 235

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  284 bits (727), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 151/243 (62%), Positives = 178/243 (73%), Gaps = 14/243 (5%)

Query: 1   MSSPYNSNWIFDCGLLDDIGV--SGGDLPS------LDPPEVLWSSSTSNPPLSAEFNDS 52
           M S  N+NWI D G  DDI V  S   LPS        PP  L S+      +SAE + S
Sbjct: 1   MVSRENTNWINDYGFYDDIPVPDSTFALPSSAFTWPTQPPFNLSSN------VSAEVDGS 54

Query: 53  FGNLDAFKETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKT 112
            G+ D  KE+GS+KRVRS SC+A+ SKACREK+RRDRLND+F+EL SIL+PGRP K DK 
Sbjct: 55  LGDSDGLKESGSKKRVRSESCAATSSKACREKLRRDRLNDKFIELGSILEPGRPAKTDKA 114

Query: 113 VLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK 172
            +L DAV+MVTQLR EAQKLK +N  L  KI ELK EKNELRDEKQRLK EKE LE+Q+K
Sbjct: 115 AILIDAVRMVTQLRGEAQKLKDANSGLQEKIKELKVEKNELRDEKQRLKAEKEKLEQQLK 174

Query: 173 ALSSQPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRP 232
           ++++ P+FLP P  +PA F+A GQ  G KLVP + YPGV+MWQFMPPAAVDTSQDHVLRP
Sbjct: 175 SMNAPPSFLPTPTALPAAFAAQGQAHGNKLVPFISYPGVAMWQFMPPAAVDTSQDHVLRP 234

Query: 233 PVA 235
           PVA
Sbjct: 235 PVA 237

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  284 bits (726), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 151/241 (62%), Positives = 184/241 (76%), Gaps = 10/241 (4%)

Query: 1   MSSPYNSNWIFDCGLLDDIGVSGGDLPSLD------PPEVLWSSSTSNPPLSAEFNDSFG 54
           M SP  +NW+++ GL++DI V   +  + +      P + L +S+     +S E + SFG
Sbjct: 1   MVSPEATNWLYEYGLIEDIPVPDSNFANTNSGFAWTPVQALNTSAN----VSGEIDGSFG 56

Query: 55  NLDAFKETGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVL 114
           + D  KETGS+KRVRS SC AS SKACREK+RRDRLND+FMEL SIL+PGRPPK DK+ +
Sbjct: 57  DSDGIKETGSKKRVRSESCGASSSKACREKLRRDRLNDKFMELGSILEPGRPPKTDKSSI 116

Query: 115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
           L DAV+MVTQLR E+QKLK SN  L  KI ELK EKNELRDEKQRLK EKE LE+Q+KA+
Sbjct: 117 LIDAVRMVTQLRGESQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKLEQQLKAM 176

Query: 175 SSQPAFLPHPPPVPAPFSAPGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPV 234
           ++QP+FLP  P +PA F+A GQ  G KLVP +GYPGV+MWQFMPPAAVDTSQDHVLRPPV
Sbjct: 177 NAQPSFLPPVPSIPAAFAAQGQAGGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPV 236

Query: 235 A 235
           A
Sbjct: 237 A 237

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 =  283 bits (724), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 143/223 (64%), Positives = 170/223 (76%), Gaps = 3/223 (1%)

Query: 16  LDDIGVSGGDLPSLDPPEVL-WSSST--SNPPLSAEFNDSFGNLDAFKETGSRKRVRSGS 72
           ++DI V GG+ P   P     W S    S+  +S E + SFG+ D  KE G RKR++  S
Sbjct: 1   MEDITVPGGEFPEPTPGTGFSWPSQALKSSSSVSLEADCSFGDSDGLKELGPRKRLKHES 60

Query: 73  CSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKL 132
           C A+G+KACREK+RRDRLN+RF+EL SIL+PGRPPK DK  +L+DAV+MVTQLR EAQKL
Sbjct: 61  CGATGTKACREKLRRDRLNERFLELGSILEPGRPPKTDKAAILSDAVRMVTQLRSEAQKL 120

Query: 133 KVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAFLPHPPPVPAPFS 192
           K SN  L  KI ELK EKNELRDEKQRLK EKE LE+QVKA+S+QP FLPHP  +PA F+
Sbjct: 121 KESNGDLQEKIKELKAEKNELRDEKQRLKAEKEKLEQQVKAISAQPGFLPHPSAMPAAFA 180

Query: 193 APGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
           A G+  G KL+P +GYP V+MWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 181 AQGRAPGNKLMPFIGYPSVAMWQFMPPAAVDTSQDHVLRPPVA 223

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	235
TAIR|locus:2157538	234	ILR3 "AT5G54680" [Arabidopsis	0.982	0.987	0.533	1.8e-55
UNIPROTKB|Q6ZKI8	253	OJ1119_D01.9 "BHLH transcripti	0.923	0.857	0.452	9.3e-43
UNIPROTKB|Q6ZGM4	236	OJ1442_E05.19 "cDNA clone:006-	0.651	0.648	0.481	9.8e-32
TAIR|locus:2086198	320	bHLH34 "AT3G23210" [Arabidopsi	0.502	0.368	0.474	1.6e-30
TAIR|locus:2129710	283	bHLH104 "AT4G14410" [Arabidops	0.617	0.512	0.437	7.1e-29
UNIPROTKB|Q67U21	343	OSJNBa0065F08.2 "Basic helix-l	0.370	0.253	0.534	1.4e-17
TAIR|locus:2092216	337	bHLH121 "AT3G19860" [Arabidops	0.370	0.258	0.477	7.1e-16
TAIR|locus:2135169	286	bHLH11 "AT4G36060" [Arabidopsi	0.370	0.304	0.443	3.3e-14
UNIPROTKB|Q2R1K8	278	Os11g0601700 "Helix-loop-helix	0.382	0.323	0.340	3e-07
UNIPROTKB|Q69V10	265	P0506F02.119 "cDNA clone:J0230	0.378	0.335	0.288	1.6e-06

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

 Score = 572 (206.4 bits), Expect = 1.8e-55, P = 1.8e-55
 Identities = 127/238 (53%), Positives = 148/238 (62%)

Query:     1 MSSPYNSNWIFDCGLLD-DIGVSGGDLPSLDPPEVLWSSSTSNPPLSAEFNDSFGNLDAF 59
             M SP N+NWI  C L+D D G      P    P       +SN   SA  + S GN +A 
Sbjct:     1 MVSPENANWI--CDLIDADYGSFTIQGPGFSWPVQQPIGVSSNS--SAGVDGSAGNSEAS 56

Query:    60 KETGSRKRVXXXXXXXXXXXXXXEKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAV 119
             KE GS+KR               EK RRDRLND+FMEL +IL+PG PPK DK  +L DAV
Sbjct:    57 KEPGSKKRGRCESSSATSSKACREKQRRDRLNDKFMELGAILEPGNPPKTDKAAILVDAV 116

Query:   120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQXX 179
             +MVTQLR EAQKLK SN  L  KI ELK EKNELRDEKQRLK EKE LE+Q+KA+++   
Sbjct:   117 RMVTQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQRLKTEKEKLEQQLKAMNAPQP 176

Query:   180 XXXXX--XXXXXXXXXXGQVVGGKLVPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
                              GQ  G K+VP++ YPGV+MWQFMPPA+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 = 452 (164.2 bits), Expect = 9.3e-43, P = 9.3e-43
 Identities = 110/243 (45%), Positives = 140/243 (57%)

Query:     8 NWIFDCGLLDDIGVSG-GDLPSLDPPEVLW--SSSTSNPPLSAEFNDSFGNLDAF--KET 62
             +W  DCG+L+D+  +  G  P        W  S S SNP  S E + S+ N  ++  KE 
Sbjct:    22 DWFLDCGILEDLPAAACGAFP--------WDASPSCSNP--SVEVS-SYVNTTSYVLKEP 70

Query:    63 GSRKRVXXXXXXXXXXXXXXEKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMV 122
             GS KRV              EK+RRD++NDRF+EL + L+PG+P K DK  +L+DA +MV
Sbjct:    71 GSNKRVRSGSCGRPTSKASREKIRRDKMNDRFLELGTTLEPGKPVKSDKAAILSDATRMV 130

Query:   123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQXXXXX 182
              QLR EA++LK +NE L  KI ELK EK+ELRDEKQ+LK EKE LE+QVK L++      
Sbjct:   131 IQLRAEAKQLKDTNESLEDKIKELKAEKDELRDEKQKLKVEKETLEQQVKILTATPAYMP 190

Query:   183 XXXXXXX---------XXXXXGQVVGGKLV-PLVGYPGVSMWQFMPPAAVDTSQDHVLRP 232
                                  GQ  G KL+ P VGYPG  MWQFMPP+ VDTS+D    P
Sbjct:   191 HPTLMPAPYPQAPLAPFHHAQGQAAGQKLMMPFVGYPGYPMWQFMPPSEVDTSKDSEACP 250

Query:   233 PVA 235
             PVA
Sbjct:   251 PVA 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 = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 78/162 (48%), Positives = 102/162 (62%)

Query:    83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
             EK+RRDRLNDRF+EL+S+++P +  K+DK  +L+DA +++ +LR EA+KLK SNEKL   
Sbjct:    75 EKIRRDRLNDRFLELSSVINPDKQAKLDKANILSDAARLLAELRGEAEKLKESNEKLRET 134

Query:   143 INELKCEKNELRDEKQRLKNEKENLERQVKALSSQXXXXXXXXXXXXXXXXXG------- 195
             I +LK EKNELRDEK  LK EKE LE+QVKALS                           
Sbjct:   135 IKDLKVEKNELRDEKVTLKAEKERLEQQVKALSVAPTGFVPHLPHPAAFHPAAFPPFIPP 194

Query:   196 -QVVGGKLVPL-VGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
              Q +G K  P    + G++MWQ++PP AVDT+QD  L PP A
Sbjct:   195 YQALGNKNAPTPAAFQGMAMWQWLPPTAVDTTQDPKLWPPNA 236

GO:0005634 "nucleus" evidence=IC

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

 Score = 282 (104.3 bits), Expect = 1.6e-30, Sum P(2) = 1.6e-30
 Identities = 56/118 (47%), Positives = 83/118 (70%)

Query:    57 DAFKETGSRKRVXXXXXXXXXXXXXXEKMRRDRLNDRFMELASILDPGRPPKMDKTVLLA 116
             + F+E  S KR               EK+RR++LND+FM+L+S+L+PGR PK DK+ +L 
Sbjct:   145 EEFEEECSGKRRRTGSCSKPGTKACREKLRREKLNDKFMDLSSVLEPGRTPKTDKSAILD 204

Query:   117 DAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
             DA+++V QLR EA +L+ +N+KLL +I  LK +KNELR+EK  LK EKE +E+Q+K++
Sbjct:   205 DAIRVVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLVLKAEKEKMEQQLKSM 262

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

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

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

 Score = 321 (118.1 bits), Expect = 7.1e-29, P = 7.1e-29
 Identities = 67/153 (43%), Positives = 98/153 (64%)

Query:    83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
             E++RR++LN+RFM+L+S+L+PGR PK DK  +L DA++++ QLRDEA KL+ +N+KLL +
Sbjct:   139 ERLRREKLNERFMDLSSVLEPGRTPKTDKPAILDDAIRILNQLRDEALKLEETNQKLLEE 198

Query:   143 INELKCEKNELRDEKQRLKNEKENLERQVKALSSQXXXXXXXXXXXXXXXXXGQVVGGKL 202
             I  LK EKNELR+EK  LK +KE  E+Q+K++++                         +
Sbjct:   199 IKSLKAEKNELREEKLVLKADKEKTEQQLKSMTAPSSGFIPHIPAAFNHNKMA------V 252

Query:   203 VPLVGYPGVSMWQFMPPAAVDTSQDHVLRPPVA 235
              P  GY  + MW +MP +  DTS+D  LRPP A
Sbjct:   253 YPSYGY--MPMWHYMPQSVRDTSRDQELRPPAA 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

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

 Score = 216 (81.1 bits), Expect = 1.4e-17, P = 1.4e-17
 Identities = 47/88 (53%), Positives = 57/88 (64%)

Query:    83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
             EKMRRDRLN++F EL S LDP RP + DK  +L+DA+QM+  L  +  KLK     L  +
Sbjct:    48 EKMRRDRLNEQFQELGSTLDPDRP-RNDKATILSDAIQMLKDLTSQVNKLKAEYTSLSEE 106

Query:   143 INELKCEKNELRDEKQRLKNEKENLERQ 170
               EL  EKNELRDEK  LK E +NL  Q
Sbjct:   107 ARELTQEKNELRDEKVSLKFEVDNLNTQ 134

GO:0005634 "nucleus" evidence=IC

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

 Score = 201 (75.8 bits), Expect = 7.1e-16, P = 7.1e-16
 Identities = 42/88 (47%), Positives = 58/88 (65%)

Query:    83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
             EK+RR++LN+ F+EL ++LDP RP K DK  +L D VQ++ +L  E  KLK     L  +
Sbjct:    67 EKLRREKLNEHFVELGNVLDPERP-KNDKATILTDTVQLLKELTSEVNKLKSEYTALTDE 125

Query:   143 INELKCEKNELRDEKQRLKNEKENLERQ 170
               EL  EKN+LR+EK  LK++ ENL  Q
Sbjct:   126 SRELTQEKNDLREEKTSLKSDIENLNLQ 153

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 = 183 (69.5 bits), Expect = 3.3e-14, P = 3.3e-14
 Identities = 39/88 (44%), Positives = 57/88 (64%)

Query:    83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
             EK+RRD+L ++F+EL + LDP RP K DK  +L D +QM+  + ++  +LK   E L  +
Sbjct:    53 EKLRRDKLKEQFLELGNALDPNRP-KSDKASVLTDTIQMLKDVMNQVDRLKAEYETLSQE 111

Query:   143 INELKCEKNELRDEKQRLKNEKENLERQ 170
               EL  EK+ELR+EK  LK++ E L  Q
Sbjct:   112 SRELIQEKSELREEKATLKSDIEILNAQ 139

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

 Score = 134 (52.2 bits), Expect = 3.0e-07, P = 3.0e-07
 Identities = 31/91 (34%), Positives = 52/91 (57%)

Query:    83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
             EK++RD+LND F+EL+S+LDP R     K  +L DA +++  L  + + L+     LL +
Sbjct:    55 EKLKRDQLNDLFVELSSMLDPERQ-NSGKATVLGDAARVLRDLVSQVESLRKEQSALLTE 113

Query:   143 INELKCEKNELRDEKQRLKNEKENLERQVKA 173
                +  E NEL++E   L+ +   L  ++ A
Sbjct:   114 RQYVGSENNELQEENIMLRAQILELHNEICA 144

GO:0005634 "nucleus" evidence=IC

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

 Score = 128 (50.1 bits), Expect = 1.6e-06, P = 1.6e-06
 Identities = 26/90 (28%), Positives = 50/90 (55%)

Query:    83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
             EK++RD+ ND F EL ++L+P R     K  +L +  +++  L  + + L+  N  L  +
Sbjct:    44 EKLKRDKQNDLFNELGNLLEPDRQNN-GKACVLGETTRILKDLLSQVESLRKENSSLKNE 102

Query:   143 INELKCEKNELRDEKQRLKNEKENLERQVK 172
              + +  E+NEL D+   L+ E   L+ +++
Sbjct:   103 SHYVALERNELHDDNSMLRTEILELQNELR 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	0.6134	0.9829	0.9871	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: grail3.0091010901 hypothetical protein (244 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	235
smart00353	53	smart00353, HLH, helix loop helix domain	4e-07
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	6e-07
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	3e-06
pfam06005	72	pfam06005, DUF904, Protein of unknown function (DU	6e-05
pfam07926	132	pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein	9e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-04
pfam12329	74	pfam12329, TMF_DNA_bd, TATA element modulatory fac	2e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-04
pfam07926	132	pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein	8e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	9e-04
pfam09744	158	pfam09744, Jnk-SapK_ap_N, JNK_SAPK-associated prot	0.001
COG3074	79	COG3074, COG3074, Uncharacterized protein conserve	0.002
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	0.003
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.003
pfam07106	169	pfam07106, TBPIP, Tat binding protein 1(TBP-1)-int	0.004
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	0.004
pfam01576	859	pfam01576, Myosin_tail_1, Myosin tail	0.004
pfam06156	106	pfam06156, DUF972, Protein of unknown function (DU	0.004
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	0.004

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

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 82  REKMRRDRLNDRFMELASILDPGRPP-KMDKTVLLADAVQMVTQLRDEAQK 131
           RE+ RR ++N+ F EL S+L       K+ K  +L  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 = 44.9 bits (107), Expect = 6e-07
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 78  SKACREKMRRDRLNDRFMELASIL-DPGRPPKMDKTVLLADAVQMVTQLRDEAQ 130
           +   RE+ RR+R+ND F EL S+L       K+ K  +L  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|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain

 Score = 42.8 bits (102), Expect = 3e-06
 Identities = 17/49 (34%), Positives = 27/49 (55%)

Query: 78  SKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLR 126
           +   RE+ RRDR+ND F EL  +L      K+ K  +L  A++ +  L+
Sbjct: 4   AHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

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

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 14/53 (26%), Positives = 29/53 (54%)

Query: 122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
           + Q  +    L++  E+L  +  +L  E  EL +E ++LK E+   + +++AL
Sbjct: 13  IQQAVETIALLQMEIEELKEENEQLSEENEELEEENKKLKEERNAWQSRLRAL 65

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

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

 Score = 40.7 bits (96), Expect = 9e-05
 Identities = 16/69 (23%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 113 VLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRD----EKQRLKNEKENLE 168
           V  A+ ++ +  LR +  +LK    +L  +    + E +E  +    +K+ L++E   LE
Sbjct: 52  VKHAEDIEELQALRKQLNELKKEIAQLKAEAESAQAELSEAEESWEEQKKMLEDELSELE 111

Query: 169 RQVKALSSQ 177
           ++++ L+ Q
Sbjct: 112 KRIEELNEQ 120

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

 Score = 42.4 bits (100), Expect = 1e-04
 Identities = 17/65 (26%), Positives = 35/65 (53%)

Query: 113 VLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK 172
            LL +  ++   LR+E  +L+    ++  ++ ELK E   L +  +RL    E+L+ ++K
Sbjct: 369 ALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELK 428

Query: 173 ALSSQ 177
            L ++
Sbjct: 429 ELEAE 433

Length = 1163

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 17/57 (29%), Positives = 29/57 (50%)

Query: 120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSS 176
           + + QL +E +KL     K    I +L+ +  EL  E   LK + E LE++++ L  
Sbjct: 12  EQIAQLMEEGEKLSKKELKHNNTIKKLRAKNKELEKEIAELKKKLEKLEKELENLEE 68

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

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 29/99 (29%), Positives = 49/99 (49%), Gaps = 13/99 (13%)

Query: 82  REKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQ---LRDEAQKLKVSNEK 138
            E+ RRD+L + + EL   L+           L A+  ++  +    RDE +  +   EK
Sbjct: 347 EERKRRDKLTEEYAELKEELE----------DLRAELEEVDKEFAETRDELKDYREKLEK 396

Query: 139 LLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQ 177
           L  +INELK E + L++E QRL  E  +L   +  + ++
Sbjct: 397 LKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAK 435

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

 Score = 38.0 bits (89), Expect = 8e-04
 Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
           L +  + + QL+ EA+  +    +      E   +K  L DE   L+   E L  Q K L
Sbjct: 68  LNELKKEIAQLKAEAESAQAELSEAEESWEE---QKKMLEDELSELEKRIEELNEQNKLL 124

Query: 175 SSQ 177
             Q
Sbjct: 125 HDQ 127

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

 Score = 39.7 bits (93), Expect = 9e-04
 Identities = 21/62 (33%), Positives = 39/62 (62%)

Query: 115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
           + +  + + +L +E ++L+   E+L  ++ EL+ EK EL DE + L+ EKE LE +++ L
Sbjct: 837 IEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELREL 896

Query: 175 SS 176
            S
Sbjct: 897 ES 898

Length = 1163

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

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 23/76 (30%), Positives = 40/76 (52%)

Query: 107 PKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKEN 166
            +++  +L  D  ++ TQ   E +  K + +KLL   +EL+ EK EL+ + + L+     
Sbjct: 48  LEVELELLREDNERLSTQYEREKELRKQAEQKLLEFEDELEQEKKELQKKIEDLEENVRQ 107

Query: 167 LERQVKALSSQPAFLP 182
           LE + K LS Q + L 
Sbjct: 108 LELKAKNLSDQVSRLE 123

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

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

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 15/57 (26%), Positives = 32/57 (56%)

Query: 118 AVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
           A+  +T L+ E ++LK  N  L  ++   + ++  L  E ++LK E+   + +++AL
Sbjct: 16  AIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEEQNGWQERLRAL 72

Length = 79

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

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 29/98 (29%), Positives = 47/98 (47%), Gaps = 14/98 (14%)

Query: 80  ACREKMRRDRL---NDRFMELASILDPGR--PPKMDKTVLLADAVQMVTQLRDEAQKLKV 134
           A     RR+RL    +R  EL +  D  R    + DK      A + + Q+ ++  +L+ 
Sbjct: 619 AELNDERRERLAEKRERKRELEAEFDEARIEEAREDK----ERAEEYLEQVEEKLDELRE 674

Query: 135 SNEKLLGKI----NELKCEKNELRDEKQRLKNEKENLE 168
             + L  +I    NEL+ E  ELR+ ++ L+N  E LE
Sbjct: 675 ERDDLQAEIGAVENELE-ELEELRERREALENRVEALE 711

Length = 880

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

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
           L +A + + +L  E Q+L+   E+L  +++EL+ E  EL+ E   L NE   LE+Q + L
Sbjct: 248 LKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQIL 307

Query: 175 SSQPAFL 181
             + A L
Sbjct: 308 RERLANL 314

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

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 5/54 (9%)

Query: 130 QKLKVSNEKLL-----GKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQP 178
           QK+ + N+         ++N+L  E  ELR+E Q LK +   LE ++K+L+S  
Sbjct: 56  QKIYLCNQDQFELPSDEELNKLDMEIEELREEVQLLKQDCSTLEIELKSLTSDL 109

This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation. Length = 169

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

 Score = 37.5 bits (88), Expect = 0.004
 Identities = 14/55 (25%), Positives = 31/55 (56%)

Query: 127 DEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAFL 181
           +  + L+  N +L  +I +L+ +  +L  E ++L+ E E L+ +++ L S P  +
Sbjct: 1   ERLEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSPPLIV 55

Length = 389

>gnl|CDD|144972 pfam01576, Myosin_tail_1, Myosin tail

 Score = 37.7 bits (88), Expect = 0.004
 Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 12/79 (15%)

Query: 110 DKTVLLADAVQMVTQLRDEAQKLKVSNEKLL----GKINEL--KCEK-----NELRDEKQ 158
           +K+ L A+   ++ QL D+  K K++ EK       +++EL  K ++     N+L  +K 
Sbjct: 153 EKSQLQAEVDDLLAQL-DQIAKAKLNAEKKAKQLESQLSELQVKLDELQRQLNDLTSQKS 211

Query: 159 RLKNEKENLERQVKALSSQ 177
           RL++E  +L RQ++   +Q
Sbjct: 212 RLQSENSDLTRQLEEAEAQ 230

The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. Length = 859

>gnl|CDD|218915 pfam06156, DUF972, Protein of unknown function (DUF972)

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 16/50 (32%), Positives = 29/50 (58%)

Query: 120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER 169
           Q + +L +E  +L++ NE L  ++ EL+ E+ E    K++L    +NL R
Sbjct: 29  QQLAELLEENAELRIENEHLRERLEELEQEQKEKEKGKKKLGEGYDNLAR 78

This family consists of several hypothetical bacterial sequences. The function of this family is unknown. Length = 106

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 37.0 bits (86), Expect = 0.004
 Identities = 27/125 (21%), Positives = 47/125 (37%), Gaps = 18/125 (14%)

Query: 83  EKMRRDRL-----NDRFMELASILDPGRPPKMDKTVLLADAVQMVTQ-LRDEAQKLKVSN 136
           E MRR +       +  +EL   L      +       AD ++   + L +EA   +   
Sbjct: 19  EDMRRAQKELEEYEETALELEEKLKQEEE-EAQLLEKKADELEEENRRLEEEAAASEEER 77

Query: 137 EKLLGKINELKCEKNELRDEKQRLKNEKENL--------ERQVKALSSQPAFL---PHPP 185
           E+L  +++E   E  +L +E+++ + E   L        E   +A             PP
Sbjct: 78  ERLEAEVDEATAEVAKLEEEREKKEAETRQLQQELREAQEAHERARQELLEAAAAPTAPP 137

Query: 186 PVPAP 190
            V AP
Sbjct: 138 HVAAP 142

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

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	99.48
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.45
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.45
smart00353	53	HLH helix loop helix domain.	99.42
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.97
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.85
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.52
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.51
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.46
KOG0561	373	consensus bHLH transcription factor [Transcription	98.07
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.91
PRK15422	79	septal ring assembly protein ZapB; Provisional	97.54
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.54
PLN03217	93	transcription factor ATBS1; Provisional	97.42
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	97.4
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	97.38
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	96.88
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	96.79
PRK15422	79	septal ring assembly protein ZapB; Provisional	96.32
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	96.27
KOG3910	632	consensus Helix loop helix transcription factor [T	96.27
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	96.05
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	96.0
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	95.92
smart00338	65	BRLZ basic region leucin zipper.	95.89
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	95.78
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	95.77
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	95.53
PRK13169	110	DNA replication intiation control protein YabA; Re	95.49
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	95.42
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	95.05
PRK11637	428	AmiB activator; Provisional	95.02
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	94.96
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	94.91
COG4026	290	Uncharacterized protein containing TOPRIM domain,	94.75
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	94.69
PRK10884	206	SH3 domain-containing protein; Provisional	94.66
PRK10884	206	SH3 domain-containing protein; Provisional	94.63
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	94.57
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	94.37
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	94.36
PRK04406	75	hypothetical protein; Provisional	94.31
PRK02119	73	hypothetical protein; Provisional	94.3
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	94.19
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	94.18
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	94.05
PRK13169	110	DNA replication intiation control protein YabA; Re	94.02
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	93.92
KOG1962	216	consensus B-cell receptor-associated protein and r	93.9
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	93.88
PF04880	166	NUDE_C: NUDE protein, C-terminal conserved region;	93.79
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	93.75
PRK00846	77	hypothetical protein; Provisional	93.6
KOG2391	365	consensus Vacuolar sorting protein/ubiquitin recep	93.37
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	93.32
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	93.28
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	93.25
KOG3119	269	consensus Basic region leucine zipper transcriptio	93.23
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	93.22
PRK11637	428	AmiB activator; Provisional	93.1
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	93.04
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	93.02
PRK00295	68	hypothetical protein; Provisional	92.92
PHA02562	562	46 endonuclease subunit; Provisional	92.92
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	92.9
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	92.82
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	92.81
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	92.59
PF10186	302	Atg14: UV radiation resistance protein and autopha	92.5
PRK02793	72	phi X174 lysis protein; Provisional	92.47
COG4467	114	Regulator of replication initiation timing [Replic	92.47
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	92.39
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	92.37
TIGR02231	525	conserved hypothetical protein. This family consis	92.17
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	92.09
KOG4571	294	consensus Activating transcription factor 4 [Trans	91.94
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	91.84
PF13815	118	Dzip-like_N: Iguana/Dzip1-like DAZ-interacting pro	91.74
smart00338	65	BRLZ basic region leucin zipper.	91.74
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	91.69
PRK04325	74	hypothetical protein; Provisional	91.63
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	91.48
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	91.42
PF10186	302	Atg14: UV radiation resistance protein and autopha	91.38
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	91.29
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	91.17
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	90.92
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	90.91
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	90.79
PF12808	52	Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2	90.74
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	90.63
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	90.56
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	90.55
PRK00736	68	hypothetical protein; Provisional	90.54
KOG3119	269	consensus Basic region leucine zipper transcriptio	90.52
COG2433	652	Uncharacterized conserved protein [Function unknow	90.44
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	90.4
PF10498	359	IFT57: Intra-flagellar transport protein 57 ; Inte	90.3
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	90.24
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	90.11
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	90.04
PRK13922	276	rod shape-determining protein MreC; Provisional	90.03
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	90.0
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	89.97
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	89.94
PRK13922	276	rod shape-determining protein MreC; Provisional	89.94
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	89.93
PF07989	75	Microtub_assoc: Microtubule associated; InterPro:	89.87
PRK09039	343	hypothetical protein; Validated	89.74
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	89.66
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	89.53
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	89.47
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	89.42
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	89.4
COG2433	652	Uncharacterized conserved protein [Function unknow	89.32
COG0497	557	RecN ATPase involved in DNA repair [DNA replicatio	89.29
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	89.27
PHA03011	120	hypothetical protein; Provisional	89.2
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	89.17
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	89.05
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	88.91
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	88.91
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	88.84
PF14662	193	CCDC155: Coiled-coil region of CCDC155	88.81
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	88.8
PRK00888	105	ftsB cell division protein FtsB; Reviewed	88.78
PRK09039	343	hypothetical protein; Validated	88.58
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	88.54
PF05008	79	V-SNARE: Vesicle transport v-SNARE protein N-termi	88.5
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	88.49
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	88.49
PF00038	312	Filament: Intermediate filament protein; InterPro:	88.34
PF15458	254	NTR2: Nineteen complex-related protein 2	88.34
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	88.31
KOG0996	1293	consensus Structural maintenance of chromosome pro	88.24
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	88.17
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	88.15
COG5570	57	Uncharacterized small protein [Function unknown]	88.11
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	88.08
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	88.04
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	88.0
TIGR02209	85	ftsL_broad cell division protein FtsL. This model	87.98
PF14282	106	FlxA: FlxA-like protein	87.96
PF14662	193	CCDC155: Coiled-coil region of CCDC155	87.95
PRK10803	263	tol-pal system protein YbgF; Provisional	87.67
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	87.65
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	87.63
COG4942	420	Membrane-bound metallopeptidase [Cell division and	87.63
PHA02562	562	46 endonuclease subunit; Provisional	87.52
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	87.47
COG1730	145	GIM5 Predicted prefoldin, molecular chaperone impl	87.44
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	87.42
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	87.27
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	87.24
COG4942	420	Membrane-bound metallopeptidase [Cell division and	87.24
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	87.09
KOG3650	120	consensus Predicted coiled-coil protein [General f	86.96
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	86.93
KOG0946	970	consensus ER-Golgi vesicle-tethering protein p115	86.8
PRK14127	109	cell division protein GpsB; Provisional	86.79
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	86.55
COG4026	290	Uncharacterized protein containing TOPRIM domain,	86.52
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	86.46
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	86.41
PRK00888	105	ftsB cell division protein FtsB; Reviewed	86.3
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	86.14
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	86.05
KOG4343	655	consensus bZIP transcription factor ATF6 [Transcri	86.04
PRK10803	263	tol-pal system protein YbgF; Provisional	85.87
PF13094	160	CENP-Q: CENP-Q, a CENPA-CAD centromere complex sub	85.73
PF11544	76	Spc42p: Spindle pole body component Spc42p; InterP	85.72
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	85.68
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	85.62
KOG4603	201	consensus TBP-1 interacting protein [Signal transd	85.59
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	85.58
PRK05771	646	V-type ATP synthase subunit I; Validated	85.48
PRK03947	140	prefoldin subunit alpha; Reviewed	85.43
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	85.37
PF07889	126	DUF1664: Protein of unknown function (DUF1664); In	85.36
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	85.26
PRK02224	880	chromosome segregation protein; Provisional	85.23
PF15397	258	DUF4618: Domain of unknown function (DUF4618)	85.0
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	84.96
TIGR01554	378	major_cap_HK97 phage major capsid protein, HK97 fa	84.92
PF05103	131	DivIVA: DivIVA protein; InterPro: IPR007793 The Ba	84.89
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	84.85
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	84.79
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	84.7
PRK04406	75	hypothetical protein; Provisional	84.68
KOG3582	856	consensus Mlx interactors and related transcriptio	84.68
KOG0249	916	consensus LAR-interacting protein and related prot	84.6
COG2919	117	Septum formation initiator [Cell division and chro	84.52
PF06103	90	DUF948: Bacterial protein of unknown function (DUF	84.4
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	84.37
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	84.29
KOG4797	123	consensus Transcriptional regulator [Transcription	83.96
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	83.9
TIGR02209	85	ftsL_broad cell division protein FtsL. This model	83.78
PRK02119	73	hypothetical protein; Provisional	83.71
PF00038	312	Filament: Intermediate filament protein; InterPro:	83.63
PF09744	158	Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; Inte	83.59
PF01166	59	TSC22: TSC-22/dip/bun family; InterPro: IPR000580	83.55
PRK14011	144	prefoldin subunit alpha; Provisional	83.51
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	83.48
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	83.36
KOG3898	254	consensus Transcription factor NeuroD and related	83.33
PF05565	162	Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840	83.24
TIGR01834	320	PHA_synth_III_E poly(R)-hydroxyalkanoic acid synth	83.08
PRK03992	389	proteasome-activating nucleotidase; Provisional	83.02
KOG3433	203	consensus Protein involved in meiotic recombinatio	82.96
PRK04325	74	hypothetical protein; Provisional	82.89
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	82.89
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	82.81
PF06103	90	DUF948: Bacterial protein of unknown function (DUF	82.73
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	82.69
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	82.6
PRK03992	389	proteasome-activating nucleotidase; Provisional	82.6
PF06785	401	UPF0242: Uncharacterised protein family (UPF0242);	82.52
PF14988	206	DUF4515: Domain of unknown function (DUF4515)	82.48
KOG4360	596	consensus Uncharacterized coiled coil protein [Fun	82.45
PF10018	188	Med4: Vitamin-D-receptor interacting Mediator subu	82.38
COG3937	108	Uncharacterized conserved protein [Function unknow	82.36
PF10458	66	Val_tRNA-synt_C: Valyl tRNA synthetase tRNA bindin	82.31
COG0216	363	PrfA Protein chain release factor A [Translation,	82.27
KOG0979	1072	consensus Structural maintenance of chromosome pro	82.14
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	82.1
PF12709	87	Kinetocho_Slk19: Central kinetochore-associated; I	81.91
PF04880	166	NUDE_C: NUDE protein, C-terminal conserved region;	81.86
KOG0612	1317	consensus Rho-associated, coiled-coil containing p	81.84
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	81.84
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	81.84
COG1256	552	FlgK Flagellar hook-associated protein [Cell motil	81.77
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	81.76
PF04325	49	DUF465: Protein of unknown function (DUF465); Inte	81.74
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	81.71
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	81.57
PRK10869	553	recombination and repair protein; Provisional	81.51
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	81.44
PF07334	76	IFP_35_N: Interferon-induced 35 kDa protein (IFP 3	81.44
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	81.37
KOG4395	285	consensus Transcription factor Atonal, contains HT	81.32
PF14282	106	FlxA: FlxA-like protein	81.27
PF04899	70	MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 Th	81.26
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	81.25
KOG1853	333	consensus LIS1-interacting protein NUDE [Cytoskele	81.23
KOG0982	502	consensus Centrosomal protein Nuf [Cell cycle cont	81.16
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	81.11
PF13747	89	DUF4164: Domain of unknown function (DUF4164)	81.07
PF02996	120	Prefoldin: Prefoldin subunit; InterPro: IPR004127	81.02
PRK05431	425	seryl-tRNA synthetase; Provisional	80.92
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	80.89
COG2919	117	Septum formation initiator [Cell division and chro	80.8
PF15290	305	Syntaphilin: Golgi-localised syntaxin-1-binding cl	80.79
PF05837	106	CENP-H: Centromere protein H (CENP-H); InterPro: I	80.72
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	80.66
PRK03947	140	prefoldin subunit alpha; Reviewed	80.61
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	80.53
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	80.52
KOG3156	220	consensus Uncharacterized membrane protein [Functi	80.28
PRK02224	880	chromosome segregation protein; Provisional	80.26
KOG1962	216	consensus B-cell receptor-associated protein and r	80.07

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

Probab=99.48  E-value=1.5e-13  Score=131.10  Aligned_cols=84  Identities=24%  Similarity=0.346  Sum_probs=68.4

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGR--PPKMDKTVLLADAVQMVTQLRDEAQKLK---VSNEKLLGKINELKCE  149 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~--~~K~dKasIL~dAI~yIk~Lr~~vq~Lk---~~n~~L~~ei~~Lk~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            6889999999999999999999999995532  2478899999999999999998877433   3445677777777777


Q ss_pred             HhHhHHHHH
Q 026702          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            777777744

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

Probab=99.45  E-value=6.4e-14  Score=97.62  Aligned_cols=51  Identities=35%  Similarity=0.539  Sum_probs=46.6

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHHhhcCCC---CCCCCchhhhHHHHHHHHHHHH
Q 026702           76 SGSKACREKMRRDRLNDRFMELASILDPG---RPPKMDKTVLLADAVQMVTQLR  126 (235)
Q Consensus        76 ~~~h~~~ERrRRdklNd~F~~Lr~lLpP~---~~~K~dKasIL~dAI~yIk~Lr  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            45799999999999999999999999764   3579999999999999999996

; 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=1.3e-13  Score=96.02  Aligned_cols=55  Identities=33%  Similarity=0.475  Sum_probs=49.6

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCC-CCCCchhhhHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGR-PPKMDKTVLLADAVQMVTQLRDEA  129 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~-~~K~dKasIL~dAI~yIk~Lr~~v  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            4678999999999999999999999995532 489999999999999999999875

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=99.42  E-value=4.3e-13  Score=92.01  Aligned_cols=51  Identities=33%  Similarity=0.503  Sum_probs=45.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhcCCCC-CCCCchhhhHHHHHHHHHHHHHHHH
Q 026702           80 ACREKMRRDRLNDRFMELASILDPGR-PPKMDKTVLLADAVQMVTQLRDEAQ  130 (235)
Q Consensus        80 ~~~ERrRRdklNd~F~~Lr~lLpP~~-~~K~dKasIL~dAI~yIk~Lr~~vq  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            46899999999999999999996543 5799999999999999999998875

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.97  E-value=1.8e-09  Score=94.62  Aligned_cols=80  Identities=19%  Similarity=0.314  Sum_probs=69.2

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCC-----CCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGRP-----PKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCE  149 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~-----~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            46789999999999999999999999944321     3899999999999999999999999999999999888887777


Q ss_pred             HhHhH
Q 026702          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            76643

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

Probab=98.85  E-value=2.2e-08  Score=89.82  Aligned_cols=82  Identities=21%  Similarity=0.229  Sum_probs=65.6

Q ss_pred             CCCCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCc-hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026702           73 CSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMD-KTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKN  151 (235)
Q Consensus        73 ~~~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~d-KasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            36799999999999999999999999999776544444 69999999999999998887777776666655555555555


Q ss_pred             HhH
Q 026702          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=98.52  E-value=5.1e-08  Score=88.14  Aligned_cols=56  Identities=32%  Similarity=0.408  Sum_probs=49.5

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHHhhcCCC-------CCCCCchhhhHHHHHHHHHHHHHHHH
Q 026702           74 SASGSKACREKMRRDRLNDRFMELASILDPG-------RPPKMDKTVLLADAVQMVTQLRDEAQ  130 (235)
Q Consensus        74 ~~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~-------~~~K~dKasIL~dAI~yIk~Lr~~vq  130 (235)
                      .++..|-..|||||+|||+++.+|+.+| +.       ...|++||-||.-|++|+++|+...+
T Consensus        31 ~rk~~Kpl~EKkRRaRIN~~L~eLK~Li-~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   31 YRKVRKPLLEKKRRARINRCLDELKDLI-PEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             HhhhcchhHHHHHHHHHHHHHHHHHHHH-HHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            5788899999999999999999999999 53       23799999999999999999997643

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

Probab=98.51  E-value=1.2e-07  Score=97.07  Aligned_cols=52  Identities=29%  Similarity=0.434  Sum_probs=48.8

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHHhhcCCCCC---CCCchhhhHHHHHHHHHHHHHH
Q 026702           76 SGSKACREKMRRDRLNDRFMELASILDPGRP---PKMDKTVLLADAVQMVTQLRDE  128 (235)
Q Consensus        76 ~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~---~K~dKasIL~dAI~yIk~Lr~~  128 (235)
                      +..|+..||||||++|..|.||++|| |.+.   -|+||-+||..||..|+.+++.
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mv-p~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMV-PTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhh-hcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            77899999999999999999999999 7776   7999999999999999999885

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.46  E-value=1.4e-07  Score=97.51  Aligned_cols=77  Identities=30%  Similarity=0.477  Sum_probs=67.8

Q ss_pred             cCCCCCCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           62 TGSRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLL  140 (235)
Q Consensus        62 ~~~~KR~r~es~~~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~  140 (235)
                      ..+.||-..+ ..++..|+..|||-|..|||+|.+|+.+| |+...|..|.+.|..||+||++|+...+.++.++..++
T Consensus       264 k~Pi~rl~~G-~~kRtAHN~IEKRYRsSINDKI~eLk~lV-~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~  340 (953)
T KOG2588|consen  264 KKPIKRLLPG-GEKRTAHNIIEKRYRSSINDKIIELKDLV-PGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR  340 (953)
T ss_pred             cCchhhcCCC-CcccchhhHHHHHhhcchhHHHHHHHHhc-CccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence            3444555543 35799999999999999999999999999 66778999999999999999999999999999998887

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.07  E-value=3.2e-06  Score=78.90  Aligned_cols=65  Identities=22%  Similarity=0.312  Sum_probs=54.5

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           76 SGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLL  140 (235)
Q Consensus        76 ~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~  140 (235)
                      +.--++-||||=.-||..|..||++||-....|.+||+||..+.+||.+|.++..+|-..|..|.
T Consensus        61 ReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn~elK  125 (373)
T KOG0561|consen   61 REIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQNGELK  125 (373)
T ss_pred             HHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccccccchHH
Confidence            44557889999999999999999999433357999999999999999999998777766665554

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

Probab=97.91  E-value=2.7e-05  Score=71.14  Aligned_cols=62  Identities=18%  Similarity=0.288  Sum_probs=51.7

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHH
Q 026702           74 SASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVS  135 (235)
Q Consensus        74 ~~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~  135 (235)
                      .++..--+|||||=.|+|+.|..|..---++-++..-|+.||-.||+||..|+.-++++.+.
T Consensus       117 DRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~  178 (284)
T KOG3960|consen  117 DRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQA  178 (284)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            56777789999999999999999987653544579999999999999999998877666543

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=97.54  E-value=0.00081  Score=51.70  Aligned_cols=60  Identities=25%  Similarity=0.448  Sum_probs=53.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            457889999999999999999999999999999999999999999999998888877763

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

Probab=97.54  E-value=8.7e-05  Score=65.41  Aligned_cols=61  Identities=21%  Similarity=0.279  Sum_probs=52.1

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHHhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHHH
Q 026702           74 SASGSKACREKMRRDRLNDRFMELASILDPGR--PPKMDKTVLLADAVQMVTQLRDEAQKLKV  134 (235)
Q Consensus        74 ~~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~--~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~  134 (235)
                      ..+..++.+||.|=..+|..|.+||..||+.-  ..|.+|+.+|.-||.||+.|..-++.-+.
T Consensus       108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~  170 (228)
T KOG4029|consen  108 AQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEA  170 (228)
T ss_pred             hhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhccccc
Confidence            35677788899999999999999999996654  46999999999999999999887665443

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.42  E-value=0.00053  Score=53.71  Aligned_cols=59  Identities=24%  Similarity=0.411  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHHHHHHhhcCCCC----CCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           84 KMRRDRLNDRFMELASILDPGR----PPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK  142 (235)
Q Consensus        84 RrRRdklNd~F~~Lr~lLpP~~----~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~e  142 (235)
                      |-=-|.|||.+..|+.+||..+    ..|.+-+-+|.++|.||+.|+.+|..|.+.+..|.+.
T Consensus        16 risddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t   78 (93)
T PLN03217         16 RISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN   78 (93)
T ss_pred             CCCHHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3345889999999999995522    3466667799999999999999999999988888654

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.40  E-value=0.0017  Score=49.38  Aligned_cols=60  Identities=25%  Similarity=0.456  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            467899999999999999999999999999999999999999999999988887777763

>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=97.38  E-value=0.0019  Score=48.63  Aligned_cols=54  Identities=30%  Similarity=0.430  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      ++.+.+|+.+++.+-.++..|+.++.+|+.+.++|.+++..|+.+.++|+++-.
T Consensus         3 ~E~l~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~   56 (72)
T PF06005_consen    3 LELLEQLEEKIQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERN   56 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            345556666666666666666666666666655555555555555555554433

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

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

Probab=96.88  E-value=0.014  Score=43.86  Aligned_cols=50  Identities=28%  Similarity=0.397  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHH
Q 026702          116 ADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKE  165 (235)
Q Consensus       116 ~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e  165 (235)
                      ..||+-|.-|+.++.+|+.+|..|.++...|+.+...|+.|...-+..+.
T Consensus        14 ~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~   63 (72)
T PF06005_consen   14 QQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLR   63 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56888888899999999998888876666666666555555444433333

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=96.79  E-value=0.0093  Score=51.36  Aligned_cols=59  Identities=24%  Similarity=0.425  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDE---AQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       115 L~dAI~yIk~Lr~~---vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      |.+.|.|+..|+..   .+.++.+|..|+.++.+|+.+..+|+.|+..|+.+..-++...++
T Consensus        82 l~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~  143 (161)
T TIGR02894        82 LQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQT  143 (161)
T ss_pred             HHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88999999999974   677888888888888888888888888888888888887776665

In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=96.32  E-value=0.035  Score=42.82  Aligned_cols=56  Identities=27%  Similarity=0.325  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHH-------HHHHHHHHHHHHHHh
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQR-------LKNEKENLERQVKAL  174 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            36788999999999999999999999999999999999776       555555555555443

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=96.27  E-value=0.045  Score=55.70  Aligned_cols=95  Identities=32%  Similarity=0.429  Sum_probs=69.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc--CCCC-CCCC---CCCC
Q 026702          114 LLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS--SQPA-FLPH---PPPV  187 (235)
Q Consensus       114 IL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~--~~p~-~~ph---~~~~  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            33344467888999999999999999999999999999999999999999999999998842  2443 5554   3344


Q ss_pred             CCCCCCCCcccCCcccccCCC
Q 026702          188 PAPFSAPGQVVGGKLVPLVGY  208 (235)
Q Consensus       188 p~~~~~~~qa~~~k~~p~~~y  208 (235)
                      |+-.-++.|+.+.-|--...|
T Consensus       167 pr~l~pp~~~~~c~lhncfdy  187 (907)
T KOG2264|consen  167 PRELEPPSQISPCQLHNCFDY  187 (907)
T ss_pred             cccCCCccccCcccchhcccc
Confidence            544445556666554333344

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=96.27  E-value=0.0043  Score=61.65  Aligned_cols=57  Identities=21%  Similarity=0.329  Sum_probs=44.9

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCC--CCCCCchhhhHHHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPG--RPPKMDKTVLLADAVQMVTQLRDEAQK  131 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~--~~~K~dKasIL~dAI~yIk~Lr~~vq~  131 (235)
                      +|..++.|||.|=..||+.|.||..+.--.  ......|-.||..|+..|..|+++|.+
T Consensus       526 RR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE  584 (632)
T KOG3910|consen  526 RRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE  584 (632)
T ss_pred             HHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH
Confidence            566677777777788999999999987221  123567899999999999999988864

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=96.05  E-value=0.12  Score=47.55  Aligned_cols=90  Identities=21%  Similarity=0.279  Sum_probs=68.1

Q ss_pred             CCch-hHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhH
Q 026702           76 SGSK-ACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELR  154 (235)
Q Consensus        76 ~~~h-~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr  154 (235)
                      +.+| ..-||.-|.||+.+..+=-+.        -.|-+-..+-=..|++|.++.+.|..+|+.|++..+.|-.+.+||+
T Consensus        60 RL~HLS~EEK~~RrKLKNRVAAQtaR--------DrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~  131 (292)
T KOG4005|consen   60 RLDHLSWEEKVQRRKLKNRVAAQTAR--------DRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELD  131 (292)
T ss_pred             hhcccCHHHHHHHHHHHHHHHHhhhh--------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence            4445 678898999998887654332        1233333333356889999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 026702          155 DEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       155 ~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .+...|+.++-.|.+|-..
T Consensus       132 ~~le~~~~~l~~~~~~~~~  150 (292)
T KOG4005|consen  132 SELELLRQELAELKQQQQH  150 (292)
T ss_pred             HHHHHHHHHHHhhHHHHHH
Confidence            9999999999888876443

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

Probab=96.00  E-value=0.041  Score=44.25  Aligned_cols=53  Identities=32%  Similarity=0.470  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcC
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSS  176 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~~  176 (235)
                      +|=..+..|++....|..++.+||.+..+|-+||+.|+-|.+.|...|.....
T Consensus         5 ~l~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~   57 (107)
T PF06156_consen    5 ELFDRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ   57 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            44556667777777777778888888888888888888888888888877544

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

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=95.92  E-value=0.049  Score=53.78  Aligned_cols=62  Identities=29%  Similarity=0.385  Sum_probs=42.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------------HHhHhHHHHHHHHHHHHHHHHHH
Q 026702          114 LLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKC----------------------EKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       114 IL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~----------------------EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      -|..-|.-+++||.+++.|..+|+.|++|.+.|++                      |..+|.+|.++|+..+..|+.||
T Consensus        60 TlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~~l  139 (472)
T TIGR03752        60 TLRTLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQRRL  139 (472)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455667788888888888888888777766655                      55555666666666666677777


Q ss_pred             HHhc
Q 026702          172 KALS  175 (235)
Q Consensus       172 k~~~  175 (235)
                      +.+.
T Consensus       140 ~~~~  143 (472)
T TIGR03752       140 AGVL  143 (472)
T ss_pred             hhcc
Confidence            6543

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.

>smart00338 BRLZ basic region leucin zipper

Probab=95.89  E-value=0.028  Score=40.38  Aligned_cols=60  Identities=28%  Similarity=0.342  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Q 026702           83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEK  157 (235)
Q Consensus        83 ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~  157 (235)
                      +|++|-++..+..+-+.-.               .--.||.+|+.+++.|+.+|..|..++..|+.|+..|++++
T Consensus         4 ~k~~rR~~rNR~aA~~~R~---------------rKk~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~   63 (65)
T smart00338        4 EKRRRRRERNREAARRSRE---------------RKKAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL   63 (65)
T ss_pred             HHHHHHHHHhHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4455555555555555443               12268888888888888888888877777777777666543

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=95.78  E-value=0.21  Score=49.45  Aligned_cols=59  Identities=19%  Similarity=0.322  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcCC
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQ  177 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~~~  177 (235)
                      ..-|.+-+.++.+|+++++.|+.|.+.|.+...+++.+...|+.|+..|+.|++++...
T Consensus        68 qSALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~~  126 (475)
T PRK13729         68 QHATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGAN  126 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcC
Confidence            34455566667777777777777777777777888888888888888888888775443

>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=95.77  E-value=0.038  Score=39.63  Aligned_cols=36  Identities=28%  Similarity=0.491  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRD  155 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~  155 (235)
                      .||.+|+.++..|+.+|..|..++..|+.+...|..
T Consensus        26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~   61 (64)
T PF00170_consen   26 QYIEELEEKVEELESENEELKKELEQLKKEIQSLKS   61 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            455556666665555555555554444444444433

; 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 ....

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

Probab=95.53  E-value=0.056  Score=45.41  Aligned_cols=55  Identities=35%  Similarity=0.528  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hHhHHHHHHHHHHHHHHHHHHHHhcC
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEK--NELRDEKQRLKNEKENLERQVKALSS  176 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~Ek--nELr~E~~~Lk~e~e~Le~qlk~~~~  176 (235)
                      |.+|+.++..|+.++..|..+...|..+.  .||+.+...|+.|++.|+..|..+..
T Consensus        81 i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~  137 (169)
T PF07106_consen   81 IKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRS  137 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            88899999999999999999988888887  67999999999999999999888654

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 [].

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=95.49  E-value=0.084  Score=42.83  Aligned_cols=51  Identities=25%  Similarity=0.375  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      +|=.++.+|++....|..++.+||.+..+|-+||..|+.|.+.|...|...
T Consensus         5 elfd~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~   55 (110)
T PRK13169          5 EIFDALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEEL   55 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            455567777777777888888888888888888888888888888888875

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

Probab=95.42  E-value=0.11  Score=41.86  Aligned_cols=57  Identities=33%  Similarity=0.424  Sum_probs=46.6

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          109 MDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       109 ~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      |||-.|.    +-|.+|.+++..|-.+...|+..+.+|-.|..+|+-||..|+..+..+++
T Consensus         1 Mdk~~l~----~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~   57 (107)
T PF06156_consen    1 MDKKELF----DRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ   57 (107)
T ss_pred             CchHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4555554    55777888888888888888888888989999999999999988888877

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

>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=95.05  E-value=0.19  Score=41.28  Aligned_cols=49  Identities=33%  Similarity=0.529  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      +..|..|..++..++.++..|+.++..|..+++++++|...|-.+.+.+
T Consensus        15 ~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~   63 (120)
T PF12325_consen   15 VQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEEL   63 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666666666666666666666666677766666655555554444

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 [].

>PRK11637 AmiB activator; Provisional

Probab=95.02  E-value=0.32  Score=46.48  Aligned_cols=61  Identities=15%  Similarity=0.188  Sum_probs=43.8

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          113 VLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       113 sIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .-+.++...|..|..++..+......++.+++.+..++++++.+...++.+++.++.+|+.
T Consensus        68 ~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~~  128 (428)
T PRK11637         68 QQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLAA  128 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445566667777777777777777777777777777777777777777777777666665

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.96  E-value=0.24  Score=37.82  Aligned_cols=52  Identities=29%  Similarity=0.374  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      .+.+.+|..+++..-.+..-|+.||++||.+.|.|..|.+.++...|.|+++
T Consensus         3 lEv~ekLE~KiqqAvdTI~LLQmEieELKEknn~l~~e~q~~q~~reaL~~e   54 (79)
T COG3074           3 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERE   54 (79)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHH
Confidence            4667889999998888889999999999999998888888777777776653

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

Probab=94.91  E-value=0.41  Score=44.46  Aligned_cols=15  Identities=13%  Similarity=0.448  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHhhc
Q 026702           87 RDRLNDRFMELASIL  101 (235)
Q Consensus        87 RdklNd~F~~Lr~lL  101 (235)
                      ...|...+..|+.+.
T Consensus       186 ~~~L~~e~~~Lk~~~  200 (325)
T PF08317_consen  186 KAELEEELENLKQLV  200 (325)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            444444444444444

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

Probab=94.75  E-value=0.22  Score=45.67  Aligned_cols=54  Identities=28%  Similarity=0.484  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +...+++.+.+++..+++.|..+..+|..+.++++++..+|..|+.+|+..++.
T Consensus       135 e~~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~  188 (290)
T COG4026         135 EDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKK  188 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            334455666777777888888888888888888888888888888888776665

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=94.69  E-value=0.26  Score=48.87  Aligned_cols=60  Identities=8%  Similarity=0.108  Sum_probs=46.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          114 LLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       114 IL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      -|.+.=.-..+|+++++.|+.+++.+..+..++...+++|.+|+..|+.+++-+..++..
T Consensus        70 ALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~~~~~  129 (475)
T PRK13729         70 ATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGANPVT  129 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcCCCC
Confidence            344444567788888888888888777777788888899999999999998776666544

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.66  E-value=0.67  Score=41.09  Aligned_cols=78  Identities=12%  Similarity=0.092  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHH
Q 026702           85 MRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEK  164 (235)
Q Consensus        85 rRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~  164 (235)
                      .|=.++...+.+|++-+ -    .     |-.+.-....+|++.++.+++....|+++...|+.|..+++.|+..|++++
T Consensus        93 ~rlp~le~el~~l~~~l-~----~-----~~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~  162 (206)
T PRK10884         93 TRVPDLENQVKTLTDKL-N----N-----IDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQL  162 (206)
T ss_pred             HHHHHHHHHHHHHHHHH-H----H-----HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33356778888888777 2    1     222233555555555555555555566666666666666666666666666


Q ss_pred             HHHHHHHH
Q 026702          165 ENLERQVK  172 (235)
Q Consensus       165 e~Le~qlk  172 (235)
                      +.++..+.
T Consensus       163 ~~~~~~~~  170 (206)
T PRK10884        163 DDKQRTII  170 (206)
T ss_pred             HHHHHHHH
Confidence            66665444

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.63  E-value=0.23  Score=44.04  Aligned_cols=32  Identities=22%  Similarity=0.264  Sum_probs=14.1

Q ss_pred             HHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          143 INELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       143 i~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      +.+|+.+..+|++|...++++.+.|+.++...
T Consensus       134 ~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~  165 (206)
T PRK10884        134 INGLKEENQKLKNQLIVAQKKVDAANLQLDDK  165 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444444444443

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.57  E-value=0.17  Score=46.81  Aligned_cols=53  Identities=23%  Similarity=0.411  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      .-|++|+++++.++.+++.|..+|.++-.+.+++++|+..+++++++|+.+|+
T Consensus        38 s~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~   90 (265)
T COG3883          38 SKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIA   90 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444554444444444444444444444444444444444444444444433

>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=94.37  E-value=0.39  Score=36.05  Aligned_cols=55  Identities=31%  Similarity=0.493  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      +.|.+|..+-++|....-++...|+.|+....++..+...|+..++.++.++..+
T Consensus        12 e~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l   66 (74)
T PF12329_consen   12 EQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESL   66 (74)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6788899888888888777778888888888888888888887777777776653

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

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=94.36  E-value=0.43  Score=35.55  Aligned_cols=55  Identities=22%  Similarity=0.324  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      -|.+|-...++|+.+|..|.++...+..|...|.+.+..-+..+|.+=..|++|.
T Consensus         8 kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rvEamI~RLk~le   62 (65)
T TIGR02449         8 QVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKVEAMITRLKALE   62 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence            3555666677777777777777777777777777777777777777777777654

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.

>PRK04406 hypothetical protein; Provisional

Probab=94.31  E-value=0.68  Score=35.03  Aligned_cols=52  Identities=15%  Similarity=0.164  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            4666777777777766667777777777777777888888888888888765

>PRK02119 hypothetical protein; Provisional

Probab=94.30  E-value=0.71  Score=34.68  Aligned_cols=54  Identities=11%  Similarity=0.110  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            345666677777776666666777777777777778888888888888888865

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

Probab=94.19  E-value=0.41  Score=41.28  Aligned_cols=82  Identities=21%  Similarity=0.280  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHH
Q 026702           85 MRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEK  164 (235)
Q Consensus        85 rRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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 RSKGELAQQLVELNDELQ-------ELEKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQL  160 (194)
T ss_dssp             ---------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccc-------hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555666666555551       1112333344556677777777777777777777777777777777777777777


Q ss_pred             HHHHHHHHH
Q 026702          165 ENLERQVKA  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            666666554

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.

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=94.18  E-value=0.41  Score=35.69  Aligned_cols=52  Identities=23%  Similarity=0.378  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------hHhHHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEK-------NELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            44566666666666666666666666655       35566777888888888887765

>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=94.05  E-value=0.64  Score=40.45  Aligned_cols=17  Identities=24%  Similarity=0.341  Sum_probs=11.1

Q ss_pred             HHHHHHHHHHHHHHhhc
Q 026702           85 MRRDRLNDRFMELASIL  101 (235)
Q Consensus        85 rRRdklNd~F~~Lr~lL  101 (235)
                      -|++=.|.+|.+|-.-|
T Consensus        59 vr~~ly~~~F~ELIRQV   75 (189)
T PF10211_consen   59 VREELYSQCFDELIRQV   75 (189)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            35566677777776655

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 [].

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=94.02  E-value=0.41  Score=38.88  Aligned_cols=57  Identities=28%  Similarity=0.346  Sum_probs=43.8

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          109 MDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       109 ~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      |||-.|.    +-|.+|.+++..|-.+...|+..+.+|-.|...|+-||..|+..++++++
T Consensus         1 Mdk~elf----d~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~   57 (110)
T PRK13169          1 MDKKEIF----DALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA   57 (110)
T ss_pred             CchhHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            4554443    45667788888888888888888888888888888888888888888744

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

Probab=93.92  E-value=0.19  Score=34.64  Aligned_cols=40  Identities=25%  Similarity=0.469  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          132 LKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       132 Lk~~n~~L~~ei~~Lk~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            3444444444444444444455555555555555554433

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

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

Probab=93.90  E-value=0.76  Score=41.41  Aligned_cols=62  Identities=26%  Similarity=0.273  Sum_probs=51.3

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          112 TVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       112 asIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .+=......=++.|+.++++.+.+.++++.+...|+.+.+++.+|-.+|..|-++|+.|+..
T Consensus       150 ~~~~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~~  211 (216)
T KOG1962|consen  150 EEENDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIES  211 (216)
T ss_pred             hhhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHhc
Confidence            44445555667778888888888888888889999999999999999999999999999875

>smart00787 Spc7 Spc7 kinetochore protein

Probab=93.88  E-value=0.78  Score=42.99  Aligned_cols=82  Identities=22%  Similarity=0.254  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHH
Q 026702           85 MRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEK  164 (235)
Q Consensus        85 rRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~  164 (235)
                      .|.+.|+..+..|+.+...-   ..-..+.|..+-.-|+.+..++...+...+.++.+...++..+++..++++.+..+|
T Consensus       179 ~~~~~L~~e~~~L~~~~~e~---~~~d~~eL~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I  255 (312)
T smart00787      179 DRKDALEEELRQLKQLEDEL---EDCDPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEI  255 (312)
T ss_pred             HHHHHHHHHHHHHHHhHHHH---HhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555555544220   111234444444444444433333333333333333333333333333333443333


Q ss_pred             HHHHH
Q 026702          165 ENLER  169 (235)
Q Consensus       165 e~Le~  169 (235)
                      ..++.
T Consensus       256 ~~ae~  260 (312)
T smart00787      256 AEAEK  260 (312)
T ss_pred             HHHHH
Confidence            33333

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

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

Probab=93.79  E-value=0.099  Score=45.22  Aligned_cols=44  Identities=30%  Similarity=0.438  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      +++.+..+-=+.|.-|++|+    .||+.|+.+.|+||-|+..|+++|
T Consensus         4 D~EsklN~AIERnalLE~EL----dEKE~L~~~~QRLkDE~RDLKqEl   47 (166)
T PF04880_consen    4 DFESKLNQAIERNALLESEL----DEKENLREEVQRLKDELRDLKQEL   47 (166)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH----HHHHHHHHCH--------------
T ss_pred             HHHHHHHHHHHHhHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444445555554    445555555555555555555554

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.

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.75  E-value=0.5  Score=43.71  Aligned_cols=66  Identities=20%  Similarity=0.314  Sum_probs=54.9

Q ss_pred             CCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          108 KMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       108 K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ..++-+.|.++-.-.+.++.+++.|....+.++.++.+++.+.+++..|...|+.+|+.|+..|..
T Consensus        33 i~~~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~~   98 (265)
T COG3883          33 IQNQDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVE   98 (265)
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445667788888999999999999999999999888888888888888888888888887775544

>PRK00846 hypothetical protein; Provisional

Probab=93.60  E-value=0.99  Score=34.61  Aligned_cols=51  Identities=14%  Similarity=0.040  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      |..++..|+....-.+.-|.+|...+-+.+.....|+.++..|..+|+.+.
T Consensus        11 le~Ri~~LE~rlAfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~~   61 (77)
T PRK00846         11 LEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKVR   61 (77)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            445555566555555555666777777777777788888888888888864

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

Probab=93.37  E-value=0.38  Score=46.08  Aligned_cols=47  Identities=32%  Similarity=0.353  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcCCC
Q 026702          132 LKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQP  178 (235)
Q Consensus       132 Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~~~p  178 (235)
                      .+++.+.++.+...||+-.+||+.-++.|+.++++||||+..++.+-
T Consensus       223 ~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~ni  269 (365)
T KOG2391|consen  223 REEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQKNI  269 (365)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhhh
Confidence            34455555555666667677777777777777777777766654433

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=93.32  E-value=0.95  Score=38.27  Aligned_cols=70  Identities=29%  Similarity=0.447  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAFLPHP  184 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~~~p~~~ph~  184 (235)
                      .+.++.-+..+++....+..++..+..++.....+...+|++...++.+.+++..+...+...-+.+..|
T Consensus        72 ~~~~v~~L~h~keKl~~~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~~~~~~~l~~~~~~~~~P  141 (177)
T PF13870_consen   72 IGKTVQILTHVKEKLHFLSEELERLKQELKDREEELAKLREELYRVKKERDKLRKQNKKLRQQGGLLGVP  141 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCc
Confidence            3567778888888888888889999999999999999999999999999999999988876655544443

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

Probab=93.28  E-value=0.36  Score=45.00  Aligned_cols=16  Identities=31%  Similarity=0.360  Sum_probs=6.5

Q ss_pred             HHHHHHHHHHHHHHHH
Q 026702          158 QRLKNEKENLERQVKA  173 (235)
Q Consensus       158 ~~Lk~e~e~Le~qlk~  173 (235)
                      ..|+.+++...++|..
T Consensus       116 ~sl~~q~~~~~~~L~~  131 (314)
T PF04111_consen  116 DSLKNQYEYASNQLDR  131 (314)
T ss_dssp             HHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3344444444444443

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.

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=93.25  E-value=0.86  Score=33.95  Aligned_cols=53  Identities=21%  Similarity=0.345  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            56788888888888888888888888888888888888888888777788775

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.

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

Probab=93.23  E-value=0.99  Score=41.30  Aligned_cols=26  Identities=23%  Similarity=0.427  Sum_probs=10.1

Q ss_pred             HHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          147 KCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       147 k~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      ...+.+|..||..|+.+++.|++++.
T Consensus       221 ~~r~~~leken~~lr~~v~~l~~el~  246 (269)
T KOG3119|consen  221 AHRVAELEKENEALRTQVEQLKKELA  246 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333334444444443333

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=93.22  E-value=0.061  Score=46.45  Aligned_cols=53  Identities=25%  Similarity=0.272  Sum_probs=45.2

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRD  127 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~  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            57779999999999999999999999943234699999999999999887643

>PRK11637 AmiB activator; Provisional

Probab=93.10  E-value=0.97  Score=43.19  Aligned_cols=32  Identities=28%  Similarity=0.345  Sum_probs=13.0

Q ss_pred             HHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          142 KINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       142 ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ++..+..+++++..+...|+.+++.++.+|..
T Consensus        90 ~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~  121 (428)
T PRK11637         90 KLRETQNTLNQLNKQIDELNASIAKLEQQQAA  121 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333334444444444444444444433

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

Probab=93.04  E-value=0.8  Score=42.57  Aligned_cols=12  Identities=25%  Similarity=0.573  Sum_probs=5.3

Q ss_pred             HHHHHHHHHhhc
Q 026702           90 LNDRFMELASIL  101 (235)
Q Consensus        90 lNd~F~~Lr~lL  101 (235)
                      |......|..++
T Consensus       168 L~~~~~~l~~~~  179 (325)
T PF08317_consen  168 LDKQLEQLDELL  179 (325)
T ss_pred             HHHHHHHHHHHH
Confidence            334444444444

>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=93.02  E-value=0.86  Score=32.58  Aligned_cols=37  Identities=35%  Similarity=0.487  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          135 SNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       135 ~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      ....|+.++..|..+...|+.++..|+.++..|..++
T Consensus        27 ~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~   63 (64)
T PF00170_consen   27 YIEELEEKVEELESENEELKKELEQLKKEIQSLKSEN   63 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3444555555555555556666666666666665554

; 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 ....

>PRK00295 hypothetical protein; Provisional

Probab=92.92  E-value=1.4  Score=32.64  Aligned_cols=49  Identities=14%  Similarity=0.108  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          127 DEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       127 ~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      .++..|+....-++..|.+|...+-+.+.+...|+.++..|..+|+.+.
T Consensus         5 ~Ri~~LE~kla~qE~tie~Ln~~v~~Qq~~I~~L~~ql~~L~~rl~~~~   53 (68)
T PRK00295          5 ERVTELESRQAFQDDTIQALNDVLVEQQRVIERLQLQMAALIKRQEEMV   53 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3444555555444455555556666666666677777777777777764

>PHA02562 46 endonuclease subunit; Provisional

Probab=92.92  E-value=0.95  Score=43.84  Aligned_cols=76  Identities=14%  Similarity=0.198  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHH
Q 026702           86 RRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKE  165 (235)
Q Consensus        86 RRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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 EFNEQSKKLLELKNKI---S----TNKQSLITLVDKAKKVKAAIEELQAEFVDNAEELAKLQDELDKIVKTKSELVKEKY  403 (562)
T ss_pred             HHHHHHHHHHHHHHHH---H----HHHHHHHHHHHHHHHHHHHHHHHHhhhhchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566677777777777   1    11222777888888999999999888888888888888888888888777777766


Q ss_pred             HHH
Q 026702          166 NLE  168 (235)
Q Consensus       166 ~Le  168 (235)
                      ..+
T Consensus       404 ~~~  406 (562)
T PHA02562        404 HRG  406 (562)
T ss_pred             HHH
Confidence            543

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

Probab=92.90  E-value=0.87  Score=39.98  Aligned_cols=61  Identities=20%  Similarity=0.365  Sum_probs=44.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          113 VLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       113 sIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .|..+=+..|+.|+.++..++..-......+.++..|...|.+....+..+++.|+.+|+.
T Consensus        20 dIT~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~   80 (201)
T PF13851_consen   20 DITLNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKN   80 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            3666778889999988888887666666666666777666777777777777777766654

>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=92.82  E-value=0.55  Score=39.42  Aligned_cols=48  Identities=27%  Similarity=0.434  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHH--HHHHHHHHHHHHHHH
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCEKNELRDEK--QRLKNEKENLERQVK  172 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~--~~Lk~e~e~Le~qlk  172 (235)
                      |..++..|+.++..|..+++.|+.|...|..+.  ..|..+++.|+.+++
T Consensus        77 ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~  126 (169)
T PF07106_consen   77 LDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIE  126 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333333333331  233334444444333

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 [].

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=92.81  E-value=0.077  Score=53.60  Aligned_cols=47  Identities=34%  Similarity=0.340  Sum_probs=38.9

Q ss_pred             CchhHHHHHHHHHHHHHHHHHHhhcCC--CCCCCCchhhhHHHHHHHHH
Q 026702           77 GSKACREKMRRDRLNDRFMELASILDP--GRPPKMDKTVLLADAVQMVT  123 (235)
Q Consensus        77 ~~h~~~ERrRRdklNd~F~~Lr~lLpP--~~~~K~dKasIL~dAI~yIk  123 (235)
                      .+|.---||-|||||.-+..|.++||=  +.++|.||-|||.=++.|++
T Consensus        27 ~tkSNPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   27 LTKSNPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             cccCCcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            345555688999999999999999932  33579999999999999976

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

Probab=92.59  E-value=0.74  Score=33.93  Aligned_cols=51  Identities=20%  Similarity=0.268  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~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            455666666666666666666667777777777777777777778877765

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.

>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=92.50  E-value=0.8  Score=40.35  Aligned_cols=11  Identities=18%  Similarity=0.296  Sum_probs=4.1

Q ss_pred             HHHHHHHHHHH
Q 026702          163 EKENLERQVKA  173 (235)
Q Consensus       163 e~e~Le~qlk~  173 (235)
                      +++.++.++..
T Consensus       127 ~~~~~~~~l~~  137 (302)
T PF10186_consen  127 ELEERKQRLSQ  137 (302)
T ss_pred             HHHHHHHHHHH
Confidence            33333334333

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

>PRK02793 phi X174 lysis protein; Provisional

Probab=92.47  E-value=2  Score=32.15  Aligned_cols=51  Identities=20%  Similarity=0.141  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~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            555566666666666666666667777777777777778888888888764

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

Probab=92.47  E-value=0.69  Score=37.84  Aligned_cols=50  Identities=24%  Similarity=0.343  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            34456677788888888889999999999999999999999999988865

>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=92.39  E-value=0.45  Score=32.82  Aligned_cols=37  Identities=38%  Similarity=0.477  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHH
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLK  161 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk  161 (235)
                      |+..-..|+...+.|..+...|+.|++.|+.|...|+
T Consensus         3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~   39 (45)
T PF02183_consen    3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELK   39 (45)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333344444444444444444444444444444443

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

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

Probab=92.37  E-value=1.6  Score=35.87  Aligned_cols=64  Identities=25%  Similarity=0.332  Sum_probs=39.6

Q ss_pred             chhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHH---HHHHHHHHHHHHHH
Q 026702          110 DKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQR---LKNEKENLERQVKA  173 (235)
Q Consensus       110 dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~---Lk~e~e~Le~qlk~  173 (235)
                      .-.+++..=-.-|+++..++..|+.++..|..+-+.+..|+-.|..++..   +..++..|+.+++.
T Consensus        13 ~~~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~~~~~~~~~~L~~el~~   79 (120)
T PF12325_consen   13 PSVQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEELRALKKEVEELEQELEE   79 (120)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44556666666777788888888887777776666666666655555532   23344444444443

The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].

>TIGR02231 conserved hypothetical protein

Probab=92.17  E-value=1.1  Score=43.99  Aligned_cols=87  Identities=18%  Similarity=0.220  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHH
Q 026702           86 RRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDE---------------AQKLKVSNEKLLGKINELKCEK  150 (235)
Q Consensus        86 RRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~---------------vq~Lk~~n~~L~~ei~~Lk~Ek  150 (235)
                      +...|.+.+.+|..-+.    .-.++...+..-+.+|..+...               +.++.+-.....+++.++..++
T Consensus        72 ~~~~l~~~l~~l~~~~~----~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (525)
T TIGR02231        72 RLAELRKQIRELEAELR----DLEDRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTED  147 (525)
T ss_pred             HHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455566666666551    2345667777777777777632               3445555566666777777777


Q ss_pred             hHhHHHHHHHHHHHHHHHHHHHHhcC
Q 026702          151 NELRDEKQRLKNEKENLERQVKALSS  176 (235)
Q Consensus       151 nELr~E~~~Lk~e~e~Le~qlk~~~~  176 (235)
                      .++..+...|+.++++|+++|..++.
T Consensus       148 ~~~~~~~~~~~~~l~~l~~~l~~l~~  173 (525)
T TIGR02231       148 REAERRIRELEKQLSELQNELNALLT  173 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            77777777777788888887776543

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.

>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=92.09  E-value=2.1  Score=40.55  Aligned_cols=68  Identities=21%  Similarity=0.356  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHHhh--------cCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhH
Q 026702           86 RRDRLNDRFMELASI--------LDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELR  154 (235)
Q Consensus        86 RRdklNd~F~~Lr~l--------LpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr  154 (235)
                      |...++....+|--.        ++|.. .+.+=+.+|.++-+-.+.|+.++..|++....++.+++-|+...+..|
T Consensus        38 r~q~LKkk~~el~~~~~~~~d~~~~~~~-~~~~La~lL~~sre~Nk~L~~Ev~~Lrqkl~E~qGD~KlLR~~la~~r  113 (319)
T PF09789_consen   38 RYQALKKKYRELIQEAAGFGDPSIPPEK-ENKNLAQLLSESREQNKKLKEEVEELRQKLNEAQGDIKLLREKLARQR  113 (319)
T ss_pred             HHHHHHHHHHHhhhhhcccCCccCCccc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHhhh
Confidence            446666666666521        21322 345556788999999999999999999988888888777777665444

>KOG4571 consensus Activating transcription factor 4 [Transcription]

Probab=91.94  E-value=1.4  Score=41.41  Aligned_cols=50  Identities=26%  Similarity=0.412  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          117 DAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       117 dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      -|.+|=+.-|.       +.+.|..|++.|.++..+|++..+.|..||.+|+|-|..
T Consensus       238 AAtRYRqKkRa-------e~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e  287 (294)
T KOG4571|consen  238 AATRYRQKKRA-------EKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILE  287 (294)
T ss_pred             HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56777443333       334455556666666667777777777777777776554

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=91.84  E-value=1.1  Score=38.87  Aligned_cols=51  Identities=25%  Similarity=0.316  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      ...+.|+.+.+.|+.++..|+.+++.|..|...|..+...++.+-+-|-.-
T Consensus        97 ~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~I  147 (161)
T TIGR02894        97 PSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDI  147 (161)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566667777777777777777777777777766666666665555443

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.

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

Probab=91.74  E-value=1.2  Score=35.75  Aligned_cols=55  Identities=20%  Similarity=0.331  Sum_probs=33.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          114 LLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       114 IL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      ++.=+|+|+-..++   .|...+..|+++++.+..+..+|+.+...++.++..|+.++
T Consensus        63 LaQl~ieYLl~~q~---~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~  117 (118)
T PF13815_consen   63 LAQLSIEYLLHCQE---YLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKES  117 (118)
T ss_pred             HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            44556777665554   34444556666666666666666666666666666666554

>smart00338 BRLZ basic region leucin zipper

Probab=91.74  E-value=1.8  Score=30.89  Aligned_cols=35  Identities=34%  Similarity=0.589  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          137 EKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       137 ~~L~~ei~~Lk~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            34444555555555555555555555555555544

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

Probab=91.69  E-value=0.88  Score=36.13  Aligned_cols=50  Identities=24%  Similarity=0.331  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHH--HHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          123 TQLRDEAQKLKVSNEKL--LGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L--~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      .++..+++.++.+.+.|  ..++..|+.+..+++-+...|.++++.+.+++.
T Consensus        45 ~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~~~~~   96 (106)
T PF10805_consen   45 DEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVSHQLD   96 (106)
T ss_pred             HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            34455566666666555  455666666666666666666666666555544

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

>PRK04325 hypothetical protein; Provisional

Probab=91.63  E-value=2.7  Score=31.61  Aligned_cols=52  Identities=13%  Similarity=0.155  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      .+..++..|+....-++..|.+|...+-+.+.+...|+.++..|..+|+.+.
T Consensus         6 ~~e~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl~~~~   57 (74)
T PRK04325          6 EMEDRITELEIQLAFQEDLIDGLNATVARQQQTLDLLQAQLRLLYQQMRDAN   57 (74)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3445555666655555555666666666666677777777777777777765

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

Probab=91.48  E-value=1.1  Score=39.90  Aligned_cols=8  Identities=38%  Similarity=1.232  Sum_probs=4.3

Q ss_pred             cccccCCC
Q 026702          212 SMWQFMPP  219 (235)
Q Consensus       212 ~mwq~~pp  219 (235)
                      .=|+|+|.
T Consensus       212 ~~W~~l~~  219 (251)
T PF11932_consen  212 GQWQWLPD  219 (251)
T ss_pred             CCCeECCH
Confidence            34666554

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.

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

Probab=91.42  E-value=1.2  Score=40.62  Aligned_cols=51  Identities=16%  Similarity=0.320  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      +..|=++.++.|..|++|+..++.++..|+.|...|+++..+|-.+++-+.
T Consensus        84 VtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylq  134 (248)
T PF08172_consen   84 VTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQ  134 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344555566666666666666666777777777777777777777766643

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

>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=91.38  E-value=3.5  Score=36.29  Aligned_cols=22  Identities=27%  Similarity=0.377  Sum_probs=11.9

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHH
Q 026702          152 ELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       152 ELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ++.++....+.....++.++..
T Consensus       123 ~~~~~~~~~~~~l~~l~~~l~~  144 (302)
T PF10186_consen  123 ELQNELEERKQRLSQLQSQLAR  144 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3444445555565556666554

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

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

Probab=91.29  E-value=2.7  Score=32.44  Aligned_cols=44  Identities=32%  Similarity=0.380  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      +|..++..|+..+..|-..|..++.|...|+.||..|+.=|..|
T Consensus        20 ~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nL   63 (80)
T PF10224_consen   20 ELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNL   63 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444444444444333333

The exact function is unknown.

>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=91.17  E-value=0.61  Score=32.52  Aligned_cols=29  Identities=38%  Similarity=0.565  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          141 GKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       141 ~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (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            34455555555566666666666655554

; 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 ....

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

Probab=90.92  E-value=1.1  Score=32.25  Aligned_cols=42  Identities=36%  Similarity=0.555  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          131 KLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       131 ~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      +++.+...|+.+++.++.+..+|+.+...|+...+.++...+
T Consensus        21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~AR   62 (80)
T PF04977_consen   21 QLNQEIAELQKEIEELKKENEELKEEIERLKNDPDYIEKVAR   62 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            344444444444444455555555555555445555555544

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

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=90.91  E-value=1.9  Score=32.12  Aligned_cols=50  Identities=20%  Similarity=0.311  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le  168 (235)
                      .+-+.-.+.....|..+++.....+...-.+.++|++|+..|+.|++.+.
T Consensus        18 ~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~~r   67 (69)
T PF14197_consen   18 TRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEELR   67 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            33344344444555555555555566666777777777777777766554

>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=90.79  E-value=4.3  Score=36.68  Aligned_cols=17  Identities=18%  Similarity=0.313  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSN  136 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n  136 (235)
                      .+|.+++++.+.|..+.
T Consensus        32 ~~L~e~~kE~~~L~~Er   48 (230)
T PF10146_consen   32 KCLEEYRKEMEELLQER   48 (230)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            45555555555554443

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.

>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=90.74  E-value=0.97  Score=32.33  Aligned_cols=47  Identities=23%  Similarity=0.256  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            44556666666666554444556678888999999999999888775

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 [, ].

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

Probab=90.63  E-value=2.7  Score=35.79  Aligned_cols=21  Identities=38%  Similarity=0.673  Sum_probs=8.9

Q ss_pred             hHhHHHHHHHHHHHHHHHHHH
Q 026702          151 NELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       151 nELr~E~~~Lk~e~e~Le~ql  171 (235)
                      ++|+.+...|+.|+++|+++|
T Consensus        76 ~~lr~~~e~L~~eie~l~~~L   96 (177)
T PF07798_consen   76 AELRSENEKLQREIEKLRQEL   96 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444433

>TIGR00219 mreC rod shape-determining protein MreC

Probab=90.56  E-value=1.7  Score=39.99  Aligned_cols=42  Identities=21%  Similarity=0.183  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          130 QKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       130 q~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      .+|++||++|++++.+|+.+.+.   ..+.|+.|.++|++.|...
T Consensus        69 ~~l~~EN~~Lr~e~~~l~~~~~~---~~~~l~~EN~rLr~LL~~~  110 (283)
T TIGR00219        69 NNLEYENYKLRQELLKKNQQLEI---LTQNLKQENVRLRELLNSP  110 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCc
Confidence            34555666666655555333332   2223666666666666553

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.

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

Probab=90.55  E-value=0.18  Score=52.13  Aligned_cols=47  Identities=26%  Similarity=0.424  Sum_probs=38.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhcCC--CCCCCCchhhhHHHHHHHHHHHHH
Q 026702           80 ACREKMRRDRLNDRFMELASILDP--GRPPKMDKTVLLADAVQMVTQLRD  127 (235)
Q Consensus        80 ~~~ERrRRdklNd~F~~Lr~lLpP--~~~~K~dKasIL~dAI~yIk~Lr~  127 (235)
                      ..+-|-||.|=|+-|.+|..+||-  +...-.|||||+-=||.|++ ||+
T Consensus        51 RdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR-lrk   99 (768)
T KOG3558|consen   51 RDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR-LRK   99 (768)
T ss_pred             hhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH-HHH
Confidence            446789999999999999999942  12368999999999999987 443

>PRK00736 hypothetical protein; Provisional

Probab=90.54  E-value=3.8  Score=30.33  Aligned_cols=47  Identities=15%  Similarity=0.212  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          129 AQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       129 vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      +..|+....-++..|.+|...+-+-..+...|+.++..|..+|+.+.
T Consensus         7 i~~LE~klafqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~~~   53 (68)
T PRK00736          7 LTELEIRVAEQEKTIEELSDQLAEQWKTVEQMRKKLDALTERFLSLE   53 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34444444444444444555555555555666666667777776654

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

Probab=90.52  E-value=1.2  Score=40.72  Aligned_cols=33  Identities=27%  Similarity=0.388  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHH
Q 026702          123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRD  155 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~  155 (235)
                      .+++.++..|+.+|+.|+.+|..|++|...|++
T Consensus       218 ~e~~~r~~~leken~~lr~~v~~l~~el~~~~~  250 (269)
T KOG3119|consen  218 DEMAHRVAELEKENEALRTQVEQLKKELATLRR  250 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455555666666666666555555555554444

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=90.44  E-value=1  Score=46.14  Aligned_cols=44  Identities=23%  Similarity=0.359  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQ  158 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~  158 (235)
                      +..-.+-|+.|++++++|+.+|..|+.++.+|++++.+|+.+..
T Consensus       417 i~~~~~~i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~  460 (652)
T COG2433         417 ITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELE  460 (652)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445566777778888888888888877777777777766643

>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=90.40  E-value=2.5  Score=37.66  Aligned_cols=12  Identities=33%  Similarity=0.399  Sum_probs=4.6

Q ss_pred             HHHHHHHHHHHH
Q 026702          159 RLKNEKENLERQ  170 (235)
Q Consensus       159 ~Lk~e~e~Le~q  170 (235)
                      .++.++++|++|
T Consensus        81 ~q~~el~~L~~q   92 (251)
T PF11932_consen   81 SQEQELASLEQQ   92 (251)
T ss_pred             HHHHHHHHHHHH
Confidence            333333334333

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.

>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=90.30  E-value=2.5  Score=40.51  Aligned_cols=24  Identities=21%  Similarity=0.433  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCC
Q 026702          160 LKNEKENLERQVKALSSQPAFLPH  183 (235)
Q Consensus       160 Lk~e~e~Le~qlk~~~~~p~~~ph  183 (235)
                      .|.-+.+|+++++.|...-|.+-|
T Consensus       333 IKqAl~kLk~EI~qMdvrIGVleh  356 (359)
T PF10498_consen  333 IKQALTKLKQEIKQMDVRIGVLEH  356 (359)
T ss_pred             HHHHHHHHHHHHHHhhhhhheehh
Confidence            333444455566666655555444

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.

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

Probab=90.24  E-value=2.5  Score=32.71  Aligned_cols=50  Identities=34%  Similarity=0.529  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH---HHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKC---EKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~---EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +|+.+++.|+.+...+..+|..++.   +..+|..+...++.++..++.+++.
T Consensus        40 ~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~   92 (108)
T PF02403_consen   40 ELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKE   92 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555555444   2345555555555555555555544

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 ....

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

Probab=90.11  E-value=2.5  Score=33.51  Aligned_cols=55  Identities=18%  Similarity=0.305  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH--HHHHhHhHHHHHHHHHHHHHHHHHHHHhcC
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINEL--KCEKNELRDEKQRLKNEKENLERQVKALSS  176 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~L--k~EknELr~E~~~Lk~e~e~Le~qlk~~~~  176 (235)
                      +..|+..+...+.....++.+++.|  +.+.+.|+-+...++.++..|+.+|+.++.
T Consensus        37 ~~~l~~~~~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~~   93 (106)
T PF10805_consen   37 IEKLEERLDEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVSH   93 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            3445566666677777777777777  777778888888888888888888877654

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

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

Probab=90.04  E-value=1.3  Score=41.00  Aligned_cols=57  Identities=19%  Similarity=0.405  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh-cCCCCCCC
Q 026702          126 RDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL-SSQPAFLP  182 (235)
Q Consensus       126 r~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~-~~~p~~~p  182 (235)
                      +..++.+..+.+.++..+..|..+...|.....+-+.|+||.+..|+++ ++.|.||-
T Consensus       168 ~~ai~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~vRPAfmd  225 (267)
T PF10234_consen  168 KEAIKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERNQKRLQSLQSVRPAFMD  225 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHH
Confidence            3344444445555555555555555556666666777777777777775 55777663

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 [].

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=90.03  E-value=1.5  Score=39.31  Aligned_cols=39  Identities=28%  Similarity=0.418  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          131 KLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       131 ~Lk~~n~~L~~ei~~Lk~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 DLREENEELKKELLELESRLQEL----EQLEAENARLRELLNL  111 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHhcC
Confidence            33444444444444444444332    2456677777776665

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

Probab=90.00  E-value=1.3  Score=45.09  Aligned_cols=58  Identities=26%  Similarity=0.389  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          116 ADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       116 ~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ...-.-+.+|+.+++.|+.+.+.+..+++.|+.+..++.+|....+.+.++|+++++.
T Consensus       324 ~~~~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~l  381 (594)
T PF05667_consen  324 EEQEQELEELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELKL  381 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3556778888899999999999999999999999999999999999999999998876

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

Probab=89.97  E-value=8.8  Score=31.52  Aligned_cols=21  Identities=29%  Similarity=0.430  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhc
Q 026702           81 CREKMRRDRLNDRFMELASIL  101 (235)
Q Consensus        81 ~~ERrRRdklNd~F~~Lr~lL  101 (235)
                      .++...|+.+++.+..|++-+
T Consensus        48 ~r~~~~~e~l~~~~~~l~~d~   68 (151)
T PF11559_consen   48 DRDMEQREDLSDKLRRLRSDI   68 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHhHH
Confidence            467788888888888887766

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.

>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=89.94  E-value=3.2  Score=35.01  Aligned_cols=39  Identities=36%  Similarity=0.510  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          135 SNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       135 ~n~~L~~ei~~Lk~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            334455555555555555555555555555555554443

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

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=89.94  E-value=2.2  Score=38.32  Aligned_cols=48  Identities=23%  Similarity=0.328  Sum_probs=27.4

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHH
Q 026702          112 TVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNE  163 (235)
Q Consensus       112 asIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e  163 (235)
                      ..=.-+.+..+.+|+++.++|++++..|+.+..    +.+++++|+.+|+.-
T Consensus        61 ~~~~~~~~~~~~~l~~en~~L~~e~~~l~~~~~----~~~~l~~en~~L~~l  108 (276)
T PRK13922         61 VSGVFESLASLFDLREENEELKKELLELESRLQ----ELEQLEAENARLREL  108 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence            333444455566666777777777777666543    224455555555543

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

Probab=89.93  E-value=1.3  Score=40.25  Aligned_cols=61  Identities=18%  Similarity=0.223  Sum_probs=53.2

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          109 MDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       109 ~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            4556777777777778899999999999999999999999999999999999888877654

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

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

Probab=89.87  E-value=2.4  Score=32.05  Aligned_cols=23  Identities=26%  Similarity=0.277  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKIN  144 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~  144 (235)
                      +++...++.+|+.+|=.|.-.|.
T Consensus         2 lrEqe~~i~~L~KENF~LKLrI~   24 (75)
T PF07989_consen    2 LREQEEQIDKLKKENFNLKLRIY   24 (75)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHH
Confidence            34555555556555544444433

>PRK09039 hypothetical protein; Validated

Probab=89.74  E-value=2.2  Score=40.35  Aligned_cols=54  Identities=15%  Similarity=0.109  Sum_probs=32.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Q 026702          113 VLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKEN  166 (235)
Q Consensus       113 sIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~  166 (235)
                      ++.+++-.-|..|+.+++.|+.++..|+.++..++.+..+.+.....|+.+++.
T Consensus       130 ~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~  183 (343)
T PRK09039        130 QVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNV  183 (343)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555666777777777777777777766665555555555544444444443

>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=89.66  E-value=1.8  Score=31.15  Aligned_cols=32  Identities=34%  Similarity=0.308  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHh
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNEL  153 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            34555566666666666666666666666665

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

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

Probab=89.53  E-value=2.8  Score=35.83  Aligned_cols=28  Identities=29%  Similarity=0.404  Sum_probs=12.2

Q ss_pred             HHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          146 LKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       146 Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ++.|..+|++|....+.|++.|+.|.+.
T Consensus       159 ~~~ei~~lk~el~~~~~~~~~LkkQ~~~  186 (192)
T PF05529_consen  159 LSEEIEKLKKELEKKEKEIEALKKQSEG  186 (192)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444443

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

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

Probab=89.47  E-value=1.8  Score=46.68  Aligned_cols=39  Identities=26%  Similarity=0.440  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          137 EKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       137 ~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      ..|.++.++++.+..+.++|+...+.++..|..++...+
T Consensus       418 ~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~l~k~i~~~~  456 (1074)
T KOG0250|consen  418 NSLREELNEVKEKAKEEEEEKEHIEGEILQLRKKIENIS  456 (1074)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333334444444444444444444

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

Probab=89.42  E-value=1.4  Score=42.26  Aligned_cols=41  Identities=24%  Similarity=0.371  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 026702          139 LLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPA  179 (235)
Q Consensus       139 L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~~~p~  179 (235)
                      |+.+++.|+.+...++++...++.|+++++.+++.+..+|.
T Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (398)
T PTZ00454         27 LEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQSVPL   67 (398)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence            33334444444455555555566667777777777777774

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

Probab=89.40  E-value=3.5  Score=37.64  Aligned_cols=48  Identities=31%  Similarity=0.304  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      +..|..+++.+++...+|..++.+|..+..+|+++...|+.++.+++.
T Consensus        91 ~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l~~~~~~~e~  138 (239)
T COG1579          91 LRALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLERLEK  138 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444455444444444444444444444444444444444444333

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=89.32  E-value=1.4  Score=45.13  Aligned_cols=37  Identities=32%  Similarity=0.462  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDE  156 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E  156 (235)
                      +.++.|+.+++.|+.+++.|+.+|..|+.+..+++++
T Consensus       429 ~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r~  465 (652)
T COG2433         429 ETVERLEEENSELKRELEELKREIEKLESELERFRRE  465 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555555555555555555555555444433

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

Probab=89.29  E-value=5  Score=40.78  Aligned_cols=86  Identities=21%  Similarity=0.358  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCCCCCchhhh-HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHhHhHHHHH
Q 026702           83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVL-LADAVQMVTQLRDEAQKLKV---SNEKLLGKINELKCEKNELRDEKQ  158 (235)
Q Consensus        83 ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasI-L~dAI~yIk~Lr~~vq~Lk~---~n~~L~~ei~~Lk~EknELr~E~~  158 (235)
                      +=.|=+++.+|+..|+.+-        .|-.. +.+.++|..+++.+++.|..   ..+.|+.+++.++.+..+.-...+
T Consensus       295 Dp~~L~~ve~Rl~~L~~l~--------RKY~~~~~~l~~~~~~~~~el~~L~~~~~~~~~Le~~~~~l~~~~~~~A~~Ls  366 (557)
T COG0497         295 DPNRLEEVEERLFALKSLA--------RKYGVTIEDLLEYLDKIKEELAQLDNSEESLEALEKEVKKLKAELLEAAEALS  366 (557)
T ss_pred             CHHHHHHHHHHHHHHHHHH--------HHhCCCHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3356678888999998887        35555 89999999999999999886   356788888888888877777766


Q ss_pred             HHHHHHH-----HHHHHHHHhcC
Q 026702          159 RLKNEKE-----NLERQVKALSS  176 (235)
Q Consensus       159 ~Lk~e~e-----~Le~qlk~~~~  176 (235)
                      ..+...-     .+.++|+.+..
T Consensus       367 ~~R~~~A~~L~~~v~~eL~~L~M  389 (557)
T COG0497         367 AIRKKAAKELEKEVTAELKALAM  389 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCC
Confidence            5555432     34556666554

>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=89.27  E-value=2.5  Score=30.62  Aligned_cols=34  Identities=18%  Similarity=0.347  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHH
Q 026702          131 KLKVSNEKLLGKINELKCEKNELRDEKQRLKNEK  164 (235)
Q Consensus       131 ~Lk~~n~~L~~ei~~Lk~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            3333333333334444444444444444443333

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) [].

>PHA03011 hypothetical protein; Provisional

Probab=89.20  E-value=3.8  Score=33.49  Aligned_cols=60  Identities=17%  Similarity=0.270  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            455567788888888888888888888888888888888888999999999999887653

>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=89.17  E-value=3  Score=34.07  Aligned_cols=61  Identities=30%  Similarity=0.336  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcC
Q 026702          116 ADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSS  176 (235)
Q Consensus       116 ~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            3444555556667777777777777778888888888888888888888888888887643

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.

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

Probab=89.05  E-value=6.5  Score=32.27  Aligned_cols=9  Identities=11%  Similarity=0.457  Sum_probs=4.4

Q ss_pred             HHHHHHHHH
Q 026702           90 LNDRFMELA   98 (235)
Q Consensus        90 lNd~F~~Lr   98 (235)
                      ||..+..++
T Consensus         7 iN~~L~s~G   15 (151)
T PF11559_consen    7 INQQLLSRG   15 (151)
T ss_pred             HHHHHHHCC
Confidence            555555443

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.

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=88.91  E-value=3.5  Score=35.94  Aligned_cols=61  Identities=16%  Similarity=0.279  Sum_probs=48.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          113 VLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       113 sIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .=|.+++..+.+=+.....|.+-|.-|++..+..+.....|.+|+..|..+.+++..+|..
T Consensus        60 ~dLe~~l~rLeEEqqR~~~L~qvN~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~eL~~  120 (182)
T PF15035_consen   60 PDLEEALIRLEEEQQRSEELAQVNALLREQLEQARKANEALQEDLQKLTQDWERLRDELEQ  120 (182)
T ss_pred             ccHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4466677777776777788888888898888888888888888888888888887776653

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

Probab=88.91  E-value=6.3  Score=37.13  Aligned_cols=74  Identities=27%  Similarity=0.420  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHH
Q 026702           86 RRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKE  165 (235)
Q Consensus        86 RRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e  165 (235)
                      +|+.+|....++++--              .+...-+++|+.+++.|......+.+++.+|+.+.+++....+.|..+..
T Consensus        28 kR~El~~~~~~~~ekR--------------deln~kvrE~~e~~~elr~~rdeineev~elK~kR~ein~kl~eL~~~~~   93 (294)
T COG1340          28 KRDELRKEASELAEKR--------------DELNAKVRELREKAQELREERDEINEEVQELKEKRDEINAKLQELRKEYR   93 (294)
T ss_pred             HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4466666666665544              13346677777888888888888888888888888887777777777777


Q ss_pred             HHHHHHHH
Q 026702          166 NLERQVKA  173 (235)
Q Consensus       166 ~Le~qlk~  173 (235)
                      .|......
T Consensus        94 ~l~e~~~~  101 (294)
T COG1340          94 ELKEKRNE  101 (294)
T ss_pred             HHHHHhhh
Confidence            66665553

>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=88.84  E-value=4.3  Score=33.02  Aligned_cols=30  Identities=27%  Similarity=0.412  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702          116 ADAVQMVTQLRDEAQKLKVSNEKLLGKINE  145 (235)
Q Consensus       116 ~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~  145 (235)
                      .++|.-|..|+.+.+.++.....|+.+...
T Consensus        55 a~~~~~L~~lr~e~~~~~~~~~~l~~~~~~   84 (132)
T PF07926_consen   55 AEDIKELQQLREELQELQQEINELKAEAES   84 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666777777777766666666655433

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

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=88.81  E-value=3.1  Score=37.01  Aligned_cols=33  Identities=27%  Similarity=0.468  Sum_probs=19.6

Q ss_pred             HHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          142 KINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       142 ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      +...|-.++..|++||..|..+.+.|+.+.+.+
T Consensus        96 E~q~L~~~i~~Lqeen~kl~~e~~~lk~~~~eL  128 (193)
T PF14662_consen   96 EQQSLVAEIETLQEENGKLLAERDGLKKRSKEL  128 (193)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHH
Confidence            344455555566666666666666666655554

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

Probab=88.80  E-value=4.1  Score=29.61  Aligned_cols=39  Identities=23%  Similarity=0.436  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRL  160 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~L  160 (235)
                      |.+|-..|+.|.....+|..++..|+.+....++|-.+-
T Consensus         5 id~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRA   43 (56)
T PF04728_consen    5 IDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARA   43 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            556677777777777777766666666665555554443

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=88.78  E-value=1.6  Score=34.69  Aligned_cols=45  Identities=22%  Similarity=0.335  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +.+|+++++.++++|++|+.+...|+.|++       .|+...+-+|.+...
T Consensus        29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~-------~L~~~~dyiEe~AR~   73 (105)
T PRK00888         29 YWRVNDQVAAQQQTNAKLKARNDQLFAEID-------DLKGGQEAIEERARN   73 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HhhCcHHHHHHHHHH
Confidence            344555566666655555555444444444       444444666666554

>PRK09039 hypothetical protein; Validated

Probab=88.58  E-value=3.3  Score=39.13  Aligned_cols=47  Identities=11%  Similarity=0.187  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          127 DEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       127 ~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .+|+.|..+.+.|+.++..|..+++.++.+....+.+++.|++.|..
T Consensus       137 ~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~  183 (343)
T PRK09039        137 AQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNV  183 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555556666666666666666666666666666666665554

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

Probab=88.54  E-value=4  Score=34.41  Aligned_cols=50  Identities=28%  Similarity=0.431  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-------HHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELK-------CEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk-------~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            334444444444444444444444       55555555555555555555555443

The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].

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

Probab=88.50  E-value=2.2  Score=31.23  Aligned_cols=58  Identities=12%  Similarity=0.297  Sum_probs=35.7

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          109 MDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       109 ~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            466666666666666666666655555443321      4556666677777777777777765

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.

>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=88.49  E-value=7.1  Score=28.66  Aligned_cols=54  Identities=30%  Similarity=0.424  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            334455555566666666666666666665555555556665555555555543

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

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

Probab=88.49  E-value=3.8  Score=38.27  Aligned_cols=8  Identities=25%  Similarity=0.293  Sum_probs=3.0

Q ss_pred             HHHHHHHH
Q 026702          166 NLERQVKA  173 (235)
Q Consensus       166 ~Le~qlk~  173 (235)
                      .|+.|+..
T Consensus       117 sl~~q~~~  124 (314)
T PF04111_consen  117 SLKNQYEY  124 (314)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            33333333

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.

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

Probab=88.34  E-value=3  Score=37.69  Aligned_cols=29  Identities=31%  Similarity=0.344  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKI  143 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei  143 (235)
                      +..+-.-++.++..++.|..+...|+...
T Consensus       211 ~~~~~~E~~~~r~~~~~l~~el~~l~~~~  239 (312)
T PF00038_consen  211 LESAKEELKELRRQIQSLQAELESLRAKN  239 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhHhHHHHHHhhhhHhhhhhhccccch
Confidence            33344444444444444444444333333

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 ....

>PF15458 NTR2: Nineteen complex-related protein 2

Probab=88.34  E-value=5.5  Score=36.18  Aligned_cols=85  Identities=20%  Similarity=0.379  Sum_probs=45.6

Q ss_pred             CchhHHHHHHHHHHHHHHHH-----------------HHhhcCCCCC-----------CCCchhhhHHHHHHHHHHHHHH
Q 026702           77 GSKACREKMRRDRLNDRFME-----------------LASILDPGRP-----------PKMDKTVLLADAVQMVTQLRDE  128 (235)
Q Consensus        77 ~~h~~~ERrRRdklNd~F~~-----------------Lr~lLpP~~~-----------~K~dKasIL~dAI~yIk~Lr~~  128 (235)
                      .......++||..|-+.|..                 |++-. -+..           +++-.-=+|.+++   ..|+..
T Consensus       141 ka~~~~~~~rR~~i~e~I~~~~~d~~de~~~~wE~aQ~rkg~-~~~~~~~~~~~~~~ip~~tpLP~L~~~~---~rL~~~  216 (254)
T PF15458_consen  141 KAEREQKRRRREEIEEAINDDDDDSEDEERAEWEAAQLRKGM-DGLSDEKDRYKPPPIPKITPLPSLSECL---ERLRES  216 (254)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHhhc-cCCccchhccCCCCCcccCCCCchhHHH---HHHHHH
Confidence            33456677888888888877                 22222 1111           2333334555555   445555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          129 AQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       129 vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      +..|+.+...+.       ..+..|+.|+..|......|+..|+
T Consensus       217 l~~le~~~~~~~-------~~l~~l~~E~~~I~~re~elq~~l~  253 (254)
T PF15458_consen  217 LSSLEDSKSQLQ-------QQLESLEKEKEEIEEREKELQELLK  253 (254)
T ss_pred             HHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            555555555544       4444555555555556666665554

>TIGR00219 mreC rod shape-determining protein MreC

Probab=88.31  E-value=1.7  Score=39.90  Aligned_cols=49  Identities=22%  Similarity=0.264  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKEN  166 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~  166 (235)
                      +.+-+..+.+|+++.++|++++..|..+   +.....+|+.||.+|+.-++-
T Consensus        61 ~~~~~~~~~~l~~EN~~Lr~e~~~l~~~---~~~~~~~l~~EN~rLr~LL~~  109 (283)
T TIGR00219        61 ISENLKDVNNLEYENYKLRQELLKKNQQ---LEILTQNLKQENVRLRELLNS  109 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhcC
Confidence            3344445566779999999998888544   334455588888888775443

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.

>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=88.24  E-value=2.2  Score=46.60  Aligned_cols=83  Identities=20%  Similarity=0.388  Sum_probs=49.8

Q ss_pred             HHHHHHHHHhhcCCCCCCCCchh-hhHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHhHhHHHHH
Q 026702           90 LNDRFMELASILDPGRPPKMDKT-VLLADAVQMVTQLRDEAQKLKVSN----------EKLLGKINELKCEKNELRDEKQ  158 (235)
Q Consensus        90 lNd~F~~Lr~lLpP~~~~K~dKa-sIL~dAI~yIk~Lr~~vq~Lk~~n----------~~L~~ei~~Lk~EknELr~E~~  158 (235)
                      +++++.+||..+ |.-.....|. +=+.+.+..|..|..++.+++...          ..+++.|.+|+.|.++++++..
T Consensus       804 ~ee~~~~lr~~~-~~l~~~l~~~~~~~k~~~~~~~~l~~~i~~~E~~~~k~~~d~~~l~~~~~~ie~l~kE~e~~qe~~~  882 (1293)
T KOG0996|consen  804 LEERVRKLRERI-PELENRLEKLTASVKRLAELIEYLESQIAELEAAVLKKVVDKKRLKELEEQIEELKKEVEELQEKAA  882 (1293)
T ss_pred             HHHHHHHHHHhh-HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCcHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            567777777777 4221111221 123445566666777776666542          2345557888888888875555


Q ss_pred             HHHHHHHHHHHHHHHh
Q 026702          159 RLKNEKENLERQVKAL  174 (235)
Q Consensus       159 ~Lk~e~e~Le~qlk~~  174 (235)
                      . |++++.|+.++..+
T Consensus       883 K-k~~i~~lq~~i~~i  897 (1293)
T KOG0996|consen  883 K-KARIKELQNKIDEI  897 (1293)
T ss_pred             H-HHHHHHHHHHHHHh
Confidence            5 67777777766554

>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=88.17  E-value=3.5  Score=39.35  Aligned_cols=43  Identities=21%  Similarity=0.302  Sum_probs=25.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHH
Q 026702          114 LLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDE  156 (235)
Q Consensus       114 IL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            4455556666677666666666666666655555555444444

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.

>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=88.15  E-value=2.9  Score=34.08  Aligned_cols=75  Identities=28%  Similarity=0.363  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702           88 DRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus        88 dklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      ..+..++..|..-|+ +  .|++-.-.    |.-=.+|+..++.|+.++..+...+.+|.+++++++.....-|..+..|
T Consensus        12 ~el~n~La~Le~slE-~--~K~S~~eL----~kqkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le~eK~ak~~l   84 (107)
T PF09304_consen   12 NELQNRLASLERSLE-D--EKTSQGEL----AKQKDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLEDEKQAKLEL   84 (107)
T ss_dssp             --HHHHHHHHHHHHH-H--HHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH-H--HHhhHHHH----HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445566666666662 1  24443322    3333457777777777777777777888888877766655444444444


Q ss_pred             HH
Q 026702          168 ER  169 (235)
Q Consensus       168 e~  169 (235)
                      +.
T Consensus        85 ~~   86 (107)
T PF09304_consen   85 ES   86 (107)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

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.

>COG5570 Uncharacterized small protein [Function unknown]

Probab=88.11  E-value=1.7  Score=31.56  Aligned_cols=23  Identities=43%  Similarity=0.549  Sum_probs=17.6

Q ss_pred             HHhHhHHHHHHHHHHHHHHHHHH
Q 026702          149 EKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       149 EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      .+.+|...+.+||.|||+|..|.
T Consensus        34 ~i~eLKRrKL~lKeeIEkLka~~   56 (57)
T COG5570          34 AIRELKRRKLRLKEEIEKLKAQM   56 (57)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccC
Confidence            34577788888888999887663

>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=88.08  E-value=3.1  Score=35.53  Aligned_cols=35  Identities=34%  Similarity=0.476  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          136 NEKLLGKINELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       136 n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      ++++.+|+++|+.|..+...|...||.|.+.|+.+
T Consensus       156 ~~~~~~ei~~lk~el~~~~~~~~~LkkQ~~~l~~e  190 (192)
T PF05529_consen  156 NKKLSEEIEKLKKELEKKEKEIEALKKQSEGLQKE  190 (192)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            34456667777777777777777777777776654

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

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

Probab=88.04  E-value=4.6  Score=33.75  Aligned_cols=41  Identities=22%  Similarity=0.324  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHH
Q 026702          118 AVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQ  158 (235)
Q Consensus       118 AI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~  158 (235)
                      |+.-+..|+.++..|+.++..+..+|..|......|..+..
T Consensus        12 a~~r~e~~e~~~K~le~~~~~~E~EI~sL~~K~~~lE~eld   52 (143)
T PF12718_consen   12 AQDRAEELEAKVKQLEQENEQKEQEITSLQKKNQQLEEELD   52 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444455555555555555554444444444444333333

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 [].

>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=88.00  E-value=7.1  Score=29.28  Aligned_cols=60  Identities=30%  Similarity=0.391  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          114 LLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       114 IL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ++..=..--..|..+..++...+.+|+..++++..++.+|......+..+++.|+..++.
T Consensus        13 ~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l~~~l~~   72 (74)
T PF12329_consen   13 QIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESLEERLKR   72 (74)
T ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            333334444556666666667777777777777777777777777777777777776653

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.

>TIGR02209 ftsL_broad cell division protein FtsL

Probab=87.98  E-value=4.5  Score=29.84  Aligned_cols=45  Identities=27%  Similarity=0.341  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          127 DEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       127 ~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      .....+..+...++.+++.++.|.++|+.|...|.. .++++..-+
T Consensus        24 ~~~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~-~~rIe~~Ar   68 (85)
T TIGR02209        24 HQTRQLNNELQKLQLEIDKLQKEWRDLQLEVAELSR-HERIEKIAK   68 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-HHHHHHHHH
Confidence            344455555555555555555555555555555443 455555444

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.

>PF14282 FlxA: FlxA-like protein

Probab=87.96  E-value=3.4  Score=32.80  Aligned_cols=55  Identities=16%  Similarity=0.209  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGK----INELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~e----i~~Lk~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            577888888888888888887762    2333444456777777777777777666554

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=87.95  E-value=4.2  Score=36.16  Aligned_cols=60  Identities=27%  Similarity=0.308  Sum_probs=36.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          114 LLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       114 IL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ++..|...=+-|.+++..|+.....|+++.+.|-++..++..|++.|-++++.|+.+-..
T Consensus        54 s~Qqal~~aK~l~eEledLk~~~~~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~k  113 (193)
T PF14662_consen   54 SLQQALQKAKALEEELEDLKTLAKSLEEENRSLLAQARQLEKEQQSLVAEIETLQEENGK  113 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            345555555566666666666666666666666666666666666666666666665443

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=87.67  E-value=2.1  Score=38.87  Aligned_cols=49  Identities=18%  Similarity=0.309  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      +-+|+.+++.|+.++..|+..++++.-+++++.+.-..+..+++++-.+
T Consensus        56 ~~~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~dld~r~~~  104 (263)
T PRK10803         56 LTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDSLSSG  104 (263)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3455666666666666666666666666666666666666666665443

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=87.65  E-value=2.6  Score=41.95  Aligned_cols=36  Identities=25%  Similarity=0.380  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRD  155 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~  155 (235)
                      +-|+.|-.++++++.+..+|..+.+.|+.|.+.||.
T Consensus        59 DTlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~   94 (472)
T TIGR03752        59 DTLRTLVAEVKELRKRLAKLISENEALKAENERLQK   94 (472)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445555555555555555555555555555544

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.

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=87.63  E-value=4.2  Score=34.31  Aligned_cols=43  Identities=26%  Similarity=0.369  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          130 QKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       130 q~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      .+|+.++..|..+++.|+.|..+++.|...++...+.|..-.-
T Consensus        77 ~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~~~~~  119 (135)
T KOG4196|consen   77 HELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEALQNSAV  119 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            4577777777777877777777777777777777777766543

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

Probab=87.63  E-value=8  Score=38.08  Aligned_cols=18  Identities=28%  Similarity=0.481  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHhh
Q 026702           83 EKMRRDRLNDRFMELASI  100 (235)
Q Consensus        83 ERrRRdklNd~F~~Lr~l  100 (235)
                      ||.||++|-..+..+..+
T Consensus       110 ~r~qr~~La~~L~A~~r~  127 (420)
T COG4942         110 EREQRRRLAEQLAALQRS  127 (420)
T ss_pred             HHHHHHHHHHHHHHHHhc
Confidence            468888898888888774

>PHA02562 46 endonuclease subunit; Provisional

Probab=87.52  E-value=3.3  Score=40.08  Aligned_cols=13  Identities=15%  Similarity=0.353  Sum_probs=4.8

Q ss_pred             HHHHHHHHHHhhc
Q 026702           89 RLNDRFMELASIL  101 (235)
Q Consensus        89 klNd~F~~Lr~lL  101 (235)
                      .|+..+..|...+
T Consensus       310 ~l~~~l~~l~~~i  322 (562)
T PHA02562        310 ELQHSLEKLDTAI  322 (562)
T ss_pred             HHHHHHHHHHHHH
Confidence            3333333333333

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

Probab=87.47  E-value=6.1  Score=42.90  Aligned_cols=88  Identities=23%  Similarity=0.321  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHHHHHhhcCCC----CCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHH
Q 026702           84 KMRRDRLNDRFMELASILDPG----RPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQR  159 (235)
Q Consensus        84 RrRRdklNd~F~~Lr~lLpP~----~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~  159 (235)
                      |++.+.++..+..+..-+--.    ...--+|..-|...|+   .|+.++.+|+.+...+.++++....|+..++.+...
T Consensus       371 k~~~d~l~k~I~~~~~~~~~~~~~~~~e~e~k~~~L~~eve---k~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~  447 (1074)
T KOG0250|consen  371 KKEVDRLEKQIADLEKQTNNELGSELEERENKLEQLKKEVE---KLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQ  447 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            556666777777776666110    0112344445554443   355567778888888888888888888888888888


Q ss_pred             HHHHHHHHHHHHHHh
Q 026702          160 LKNEKENLERQVKAL  174 (235)
Q Consensus       160 Lk~e~e~Le~qlk~~  174 (235)
                      |+..++....+|+.+
T Consensus       448 l~k~i~~~~~~l~~l  462 (1074)
T KOG0250|consen  448 LRKKIENISEELKDL  462 (1074)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            888888887777664

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

Probab=87.44  E-value=2.8  Score=35.59  Aligned_cols=46  Identities=26%  Similarity=0.419  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNE  163 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e  163 (235)
                      ..+||+|   |++++++|+....+|++++.+|.....+++.+.+.+..+
T Consensus        92 ~~eAie~---l~k~~~~l~~~~~~l~~~l~~l~~~~~~l~~~~q~~~q~  137 (145)
T COG1730          92 ADEAIEF---LKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQQLQQK  137 (145)
T ss_pred             HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566666   678888999999999999999988888888887776443

>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=87.42  E-value=6.9  Score=27.16  Aligned_cols=29  Identities=34%  Similarity=0.420  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKC  148 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~  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            45556666666666666666655555544

; 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 ....

>TIGR00606 rad50 rad50

Probab=87.27  E-value=4.5  Score=44.25  Aligned_cols=83  Identities=18%  Similarity=0.201  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHH
Q 026702           84 KMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNE  163 (235)
Q Consensus        84 RrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e  163 (235)
                      ...++++++.+..|...+ ..  -+..|. =|..++.-..+|+.++..|+.++..+..++++++.+...|..+...+..+
T Consensus       849 ~~e~e~~~~eI~~Lq~ki-~e--l~~~kl-kl~~~l~~r~~le~~L~el~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~  924 (1311)
T TIGR00606       849 RKLIQDQQEQIQHLKSKT-NE--LKSEKL-QIGTNLQRRQQFEEQLVELSTEVQSLIREIKDAKEQDSPLETFLEKDQQE  924 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHH-HH--HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            556666777777776666 21  122333 33347777788888888888888888888888888888777777777777


Q ss_pred             HHHHHHH
Q 026702          164 KENLERQ  170 (235)
Q Consensus       164 ~e~Le~q  170 (235)
                      ++++.++
T Consensus       925 ~~~~~~~  931 (1311)
T TIGR00606       925 KEELISS  931 (1311)
T ss_pred             HHHHHHH
Confidence            7665554

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

>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=87.24  E-value=3.7  Score=41.58  Aligned_cols=8  Identities=13%  Similarity=0.559  Sum_probs=5.2

Q ss_pred             CCcccCCC
Q 026702           32 PEVLWSSS   39 (235)
Q Consensus        32 ~~f~w~~~   39 (235)
                      -+|.|...
T Consensus        54 ~Tf~Wa~~   61 (546)
T PF07888_consen   54 YTFVWAPV   61 (546)
T ss_pred             eeEEeecc
Confidence            35888753

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 [].

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

Probab=87.24  E-value=6  Score=38.96  Aligned_cols=17  Identities=6%  Similarity=0.186  Sum_probs=7.6

Q ss_pred             HHHHHHHHHHHHHHhhc
Q 026702           85 MRRDRLNDRFMELASIL  101 (235)
Q Consensus        85 rRRdklNd~F~~Lr~lL  101 (235)
                      +|++.+..-+.++..-|
T Consensus        38 ~~l~q~q~ei~~~~~~i   54 (420)
T COG4942          38 KQLKQIQKEIAALEKKI   54 (420)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            44444444444444444

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

Probab=87.09  E-value=5.8  Score=33.44  Aligned_cols=85  Identities=20%  Similarity=0.250  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHH
Q 026702           82 REKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLK  161 (235)
Q Consensus        82 ~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk  161 (235)
                      ....+-..+.+.+.++...+ .      +..+=+.+-.+....+++..+..++....+.+.++.+..+..+++++...++
T Consensus        85 ~~~~~l~~l~~el~~l~~~~-~------~~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~  157 (191)
T PF04156_consen   85 ELQQQLQQLQEELDQLQERI-Q------ELESELEKLKEDLQELRELLKSVEERLDSLDESIKELEKEIRELQKELQDSR  157 (191)
T ss_pred             hHHHHHHHHHHHHHHHHHHH-H------HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555554 1      1222222222333333344445555666666667777777777774444455


Q ss_pred             HHHHHHHHHHHH
Q 026702          162 NEKENLERQVKA  173 (235)
Q Consensus       162 ~e~e~Le~qlk~  173 (235)
                      .+.+.+..+++.
T Consensus       158 ~~~~~~~~~~~~  169 (191)
T PF04156_consen  158 EEVQELRSQLER  169 (191)
T ss_pred             HHHHHHHHHHHH
Confidence            555555554443

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 [].

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

Probab=86.96  E-value=2.9  Score=34.05  Aligned_cols=37  Identities=32%  Similarity=0.401  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702          131 KLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus       131 ~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      +|+.+++.|-+.+..+|.|.-.||.||+.|-+=||.|
T Consensus        67 ELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNL  103 (120)
T KOG3650|consen   67 ELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENL  103 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHH
Confidence            3444444444444445555555667777766555544

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

Probab=86.93  E-value=5.1  Score=35.13  Aligned_cols=15  Identities=40%  Similarity=0.618  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHHHHH
Q 026702          157 KQRLKNEKENLERQV  171 (235)
Q Consensus       157 ~~~Lk~e~e~Le~ql  171 (235)
                      ..+|+.+.+.|++++
T Consensus       161 i~~lks~~~~l~~~~  175 (190)
T PF05266_consen  161 ISRLKSEAEALKEEI  175 (190)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            334434433344433

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

Probab=86.80  E-value=3.3  Score=43.91  Aligned_cols=55  Identities=22%  Similarity=0.325  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      +.|++|..+++.|++.+..|+-+.++|..+..+...+.++|+.+.+-|+.||+-.
T Consensus       664 ~lI~~lD~~~e~lkQ~~~~l~~e~eeL~~~vq~~~s~hsql~~q~~~Lk~qLg~~  718 (970)
T KOG0946|consen  664 GLIRELDYQIENLKQMEKELQVENEELEEEVQDFISEHSQLKDQLDLLKNQLGII  718 (970)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            3344444444555555555555555555555555555667778888888888743

>PRK14127 cell division protein GpsB; Provisional

Probab=86.79  E-value=4.5  Score=32.85  Aligned_cols=29  Identities=34%  Similarity=0.523  Sum_probs=15.1

Q ss_pred             HHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          145 ELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       145 ~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .|..|+.+|++++..|+.+++.++.++..
T Consensus        41 ~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~   69 (109)
T PRK14127         41 AFQKEIEELQQENARLKAQVDELTKQVSV   69 (109)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            33444445555555555555555555554

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

Probab=86.55  E-value=1.9  Score=41.44  Aligned_cols=52  Identities=21%  Similarity=0.208  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          118 AVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       118 AI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      +-.-.+.|..+..+|+.++..|+.++++++.+.+.++.|...++.|+++|..
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (398)
T PTZ00454         13 TTHTERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQS   64 (398)
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            3344566667777777788888888888888888888888889999888865

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

Probab=86.52  E-value=10  Score=35.03  Aligned_cols=95  Identities=19%  Similarity=0.211  Sum_probs=42.8

Q ss_pred             chhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHH
Q 026702           78 SKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK-------INELKCEK  150 (235)
Q Consensus        78 ~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~e-------i~~Lk~Ek  150 (235)
                      .|...|=-|.+-=|....+--.-| .+.+.-||=-.-+.+--+-+.+++++...|.++++.|+.+       ++.|+.|+
T Consensus       101 EhiD~elvrkEl~nAlvRAGLktL-~~v~~~~d~ke~~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~  179 (290)
T COG4026         101 EHIDVELVRKELKNALVRAGLKTL-QRVPEYMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVEN  179 (290)
T ss_pred             cccCHHHHHHHHHHHHHHHHHHHH-hccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355555555544444444333333 2222233433333333333444445544555555554444       44455555


Q ss_pred             hHhHHHHHHHHHHHHHHHHHHHH
Q 026702          151 NELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       151 nELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ..|.+....|-.+..+|+..+..
T Consensus       180 s~LeE~~~~l~~ev~~L~~r~~E  202 (290)
T COG4026         180 SRLEEMLKKLPGEVYDLKKRWDE  202 (290)
T ss_pred             HHHHHHHHhchhHHHHHHHHHHH
Confidence            54444444444555555554443

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

Probab=86.46  E-value=3.7  Score=39.21  Aligned_cols=37  Identities=22%  Similarity=0.380  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDE  156 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E  156 (235)
                      .-+..|..+.++|+.+..++..+++++-.+|+++..+
T Consensus       144 ~~~~~L~~enerL~~e~~~~~~qlE~~v~~K~~~E~~  180 (342)
T PF06632_consen  144 AENEHLQKENERLESEANKLLKQLEKFVNAKEEHEED  180 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444677788888888888888888888888777776

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.

>smart00787 Spc7 Spc7 kinetochore protein

Probab=86.41  E-value=4  Score=38.35  Aligned_cols=12  Identities=33%  Similarity=0.216  Sum_probs=5.7

Q ss_pred             HHHHHHHHHhhc
Q 026702           90 LNDRFMELASIL  101 (235)
Q Consensus        90 lNd~F~~Lr~lL  101 (235)
                      |+.....|..++
T Consensus       163 L~~~~~~l~~~~  174 (312)
T smart00787      163 LMKELELLNSIK  174 (312)
T ss_pred             HHHHHHHHHHHH
Confidence            444444444444

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

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=86.30  E-value=2.9  Score=33.31  Aligned_cols=34  Identities=12%  Similarity=0.201  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          136 NEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       136 n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      ...++.++.+++++..+|+.+|..|+.|+++|+.
T Consensus        29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~   62 (105)
T PRK00888         29 YWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG   62 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            3444555566666666666666666666666655

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

Probab=86.14  E-value=3.7  Score=42.05  Aligned_cols=45  Identities=24%  Similarity=0.370  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          129 AQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       129 vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ++.|+.++..+++.+..|..+.+.|+.|+......+..|+.+|..
T Consensus        17 a~~lk~e~a~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~e   61 (617)
T PF15070_consen   17 AQQLKEESAQWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSE   61 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444555555555555555555555555555555554444

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

Probab=86.05  E-value=7.9  Score=33.34  Aligned_cols=48  Identities=23%  Similarity=0.397  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      |++|..++......++.|+.|+-.|..+.+.+.+....|+.|...|=+
T Consensus       132 ~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l~~En~~Lv~  179 (194)
T PF08614_consen  132 IKDLEEELKEKNKANEILQDELQALQLQLNMLEEKLRKLEEENRELVE  179 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444455555555666666666666666666666666666665543

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.

>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]

Probab=86.04  E-value=0.96  Score=45.85  Aligned_cols=31  Identities=26%  Similarity=0.439  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          139 LLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       139 L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      |+..+++|.+|.+.||.||..||.+++-|..
T Consensus       307 Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~  337 (655)
T KOG4343|consen  307 LEARLQALLSENEQLKKENATLKRQLDELVS  337 (655)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence            3344444444444444444444444444433

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=85.87  E-value=3.8  Score=37.22  Aligned_cols=42  Identities=12%  Similarity=0.167  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          132 LKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       132 Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      |...++.|+.||.+|+-+++++.-+...++.+-..+.++|..
T Consensus        59 l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~dld~  100 (263)
T PRK10803         59 LQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDS  100 (263)
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444444444444444444444

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

Probab=85.73  E-value=9.4  Score=31.77  Aligned_cols=66  Identities=14%  Similarity=0.070  Sum_probs=46.3

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          109 MDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       109 ~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      .+...-...+++....|+.++......++.|+++++........-.+....|+..+..++.+++..
T Consensus        16 ~~~~~~~e~ll~~~~~LE~qL~~~~~~l~lLq~e~~~~e~~le~d~~~L~~Le~~~~~~~~e~~~~   81 (160)
T PF13094_consen   16 REDSFDYEQLLDRKRALERQLAANLHQLELLQEEIEKEEAALERDYEYLQELEKNAKALEREREEE   81 (160)
T ss_pred             ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344556677788888888888877778888888777666665555555666666666666666653

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

Probab=85.72  E-value=5.7  Score=30.58  Aligned_cols=49  Identities=18%  Similarity=0.209  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      |-++...|+..+...++||..|+.-...||.+...+-.-..+|+.++..
T Consensus         3 Li~qNk~L~~kL~~K~eEI~rLn~lv~sLR~KLiKYt~LnkkLq~~~~~   51 (76)
T PF11544_consen    3 LIKQNKELKKKLNDKQEEIDRLNILVGSLRGKLIKYTELNKKLQDQLLN   51 (76)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344455555555555556666666666666655555555555554443

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.

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

Probab=85.68  E-value=6.1  Score=32.19  Aligned_cols=29  Identities=10%  Similarity=0.053  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHHHHhHhHHHHHHHHH
Q 026702          134 VSNEKLLGKINELKCEKNELRDEKQRLKN  162 (235)
Q Consensus       134 ~~n~~L~~ei~~Lk~EknELr~E~~~Lk~  162 (235)
                      ..+..|+++...+..-+++|+.+...+..
T Consensus        44 ~~l~~L~~q~~s~~qr~~eLqaki~ea~~   72 (107)
T PF09304_consen   44 NALQSLQAQNASRNQRIAELQAKIDEARR   72 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333343333333333

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.

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

Probab=85.62  E-value=17  Score=31.63  Aligned_cols=93  Identities=20%  Similarity=0.307  Sum_probs=47.8

Q ss_pred             CCCchhHHHH-----HHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREK-----MRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQM---VTQLRDEAQKLKVSNEKLLGKINEL  146 (235)
Q Consensus        75 ~~~~h~~~ER-----rRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~y---Ik~Lr~~vq~Lk~~n~~L~~ei~~L  146 (235)
                      +-.+=.|.||     +=|+.+...|.+...+..      .+.+-.+.+++..   ..+|+.++..|+.++..|..++.+|
T Consensus        73 RQVTi~C~ERGlLL~rvrde~~~~l~~y~~l~~------s~~~f~~rk~l~~e~~~~~l~~~i~~L~~e~~~L~~~~~~l  146 (189)
T PF10211_consen   73 RQVTIDCPERGLLLLRVRDEYRMTLDAYQTLYE------SSIAFGMRKALQAEQGKQELEEEIEELEEEKEELEKQVQEL  146 (189)
T ss_pred             HHHHhCcHHHhHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444557777     346777777777776662      2333333344333   3345555555555555555544444


Q ss_pred             HHHHhH---------------hHHHHHHHHHHHHHHHHHHHH
Q 026702          147 KCEKNE---------------LRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       147 k~EknE---------------Lr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +.....               ..+|...||.+...|.++|+.
T Consensus       147 ~~~~e~~ek~~~e~~~~~~k~~~~ei~~lk~~~~ql~~~l~~  188 (189)
T PF10211_consen  147 KNKCEQLEKREEELRQEEEKKHQEEIDFLKKQNQQLKAQLEQ  188 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            333332               333444555555555555543

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 [].

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

Probab=85.59  E-value=4.8  Score=35.66  Aligned_cols=53  Identities=25%  Similarity=0.396  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEK--NELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~Ek--nELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      |..|+++++.|+++......||++|....  .|++++.+.|+.+....+..|+.+
T Consensus        88 i~~l~ek~q~l~~t~s~veaEik~L~s~Lt~eemQe~i~~L~kev~~~~erl~~~  142 (201)
T KOG4603|consen   88 IVALTEKVQSLQQTCSYVEAEIKELSSALTTEEMQEEIQELKKEVAGYRERLKNI  142 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34456666666666666666666666554  467777777777777766666654

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=85.58  E-value=4.3  Score=37.62  Aligned_cols=93  Identities=30%  Similarity=0.359  Sum_probs=67.1

Q ss_pred             CCCCCCCCCCCC-------CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHH
Q 026702           63 GSRKRVRSGSCS-------ASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVS  135 (235)
Q Consensus        63 ~~~KR~r~es~~-------~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~  135 (235)
                      ..+||.|....+       ++.++..+-.--|||=+.+..++-..|   +           |-.+--..|+.+.+.|+..
T Consensus        54 ~~rKr~RL~HLS~EEK~~RrKLKNRVAAQtaRDrKKaRm~eme~~i---~-----------dL~een~~L~~en~~Lr~~  119 (292)
T KOG4005|consen   54 PKRKRRRLDHLSWEEKVQRRKLKNRVAAQTARDRKKARMEEMEYEI---K-----------DLTEENEILQNENDSLRAI  119 (292)
T ss_pred             hHHHHHhhcccCHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHH---H-----------HHHHHHHHHHHHHHHHHHH
Confidence            345666655442       233334455556777778888777666   1           3345556799999999999


Q ss_pred             HHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          136 NEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       136 n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      |+.|..+.++|..+..+|++|...|+.+.---..
T Consensus       120 n~~L~~~n~el~~~le~~~~~l~~~~~~~~~~~~  153 (292)
T KOG4005|consen  120 NESLLAKNHELDSELELLRQELAELKQQQQHNTR  153 (292)
T ss_pred             HHHHHhhhHHHHHHHHHHHHHHHhhHHHHHHhhH
Confidence            9999999999999999999999988877654333

>PRK05771 V-type ATP synthase subunit I; Validated

Probab=85.48  E-value=3.8  Score=41.33  Aligned_cols=79  Identities=25%  Similarity=0.284  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHH
Q 026702           84 KMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNE  163 (235)
Q Consensus        84 RrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e  163 (235)
                      .++.+++++.+..|+...+. .  +..+..  ...+++. .+.+-.+..+...+++.+++.+|..++++|++|...|+++
T Consensus        49 ~~~~~~~~~~l~~L~~~~~~-~--~~~~~~--~~~~~~~-~~~e~~~~~~~~~~~~~~~i~~l~~~~~~L~~~~~~l~~~  122 (646)
T PRK05771         49 RSLLTKLSEALDKLRSYLPK-L--NPLREE--KKKVSVK-SLEELIKDVEEELEKIEKEIKELEEEISELENEIKELEQE  122 (646)
T ss_pred             HHHHHHHHHHHHHHHHhccc-c--ccchhh--hcccccc-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667788888888888732 1  111000  0011111 1111122334445555556666666666666666666666


Q ss_pred             HHHHH
Q 026702          164 KENLE  168 (235)
Q Consensus       164 ~e~Le  168 (235)
                      ++.|+
T Consensus       123 ~~~l~  127 (646)
T PRK05771        123 IERLE  127 (646)
T ss_pred             HHHhh
Confidence            66555

>PRK03947 prefoldin subunit alpha; Reviewed

Probab=85.43  E-value=4.1  Score=33.04  Aligned_cols=46  Identities=28%  Similarity=0.432  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNE  163 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e  163 (235)
                      +.+|+.+   |..+++.|+...+.|..++..++.+.+++++....|..+
T Consensus        92 ~~eA~~~---l~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~l~~~  137 (140)
T PRK03947         92 LDEAIEI---LDKRKEELEKALEKLEEALQKLASRIAQLAQELQQLQQE  137 (140)
T ss_pred             HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7788877   556667777777777777777777777766666655544

>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=85.37  E-value=3.4  Score=29.95  Aligned_cols=37  Identities=19%  Similarity=0.424  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          137 EKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       137 ~~L~~ei~~Lk~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            3455566666666666666666666666666665544

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) [].

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

Probab=85.36  E-value=5.3  Score=33.17  Aligned_cols=50  Identities=12%  Similarity=0.281  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            35566666666666655556666677777777777777776666665444

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

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

Probab=85.26  E-value=6.2  Score=30.43  Aligned_cols=49  Identities=24%  Similarity=0.365  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcC
Q 026702          128 EAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSS  176 (235)
Q Consensus       128 ~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~~  176 (235)
                      +-++|.++...||..+..|-..+.+.++|+..|+.|.+-|++=+..+-.
T Consensus        17 ~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm~   65 (80)
T PF10224_consen   17 EKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLMS   65 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3557778888899999999999999999999999999999998888533

The exact function is unknown.

>PRK02224 chromosome segregation protein; Provisional

Probab=85.23  E-value=9.1  Score=39.49  Aligned_cols=23  Identities=26%  Similarity=0.380  Sum_probs=8.9

Q ss_pred             HHHhHhHHHHHHHHHHHHHHHHH
Q 026702          148 CEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       148 ~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      ..++.++.+...|+.+++.++.+
T Consensus       377 ~~l~~~~~~l~~l~~el~el~~~  399 (880)
T PRK02224        377 EAVEDRREEIEELEEEIEELRER  399 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333444444444333

>PF15397 DUF4618: Domain of unknown function (DUF4618)

Probab=85.00  E-value=4.4  Score=37.46  Aligned_cols=83  Identities=23%  Similarity=0.296  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Q 026702           88 DRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQ-LRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKEN  166 (235)
Q Consensus        88 dklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~-Lr~~vq~Lk~~n~~L~~ei~~Lk~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 DELNEMRQMELASL-S-RKIQEKKEEILSSAAEKTQSPMQPALLQRTLENQVMQKEIVQFREEIDELEEEIPQLRAEVEQ  218 (258)
T ss_pred             HHHHHHHHHHHHHH-H-HHHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555544 2 11244667788876655444 555555555678888888888888888888888888888888


Q ss_pred             HHHHHH
Q 026702          167 LERQVK  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            888776

>TIGR00606 rad50 rad50

Probab=84.96  E-value=7.1  Score=42.77  Aligned_cols=85  Identities=9%  Similarity=0.188  Sum_probs=51.8

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHH------HHHHHHHHHHHHHHH-----HHHHHHHHHHHHHhHh
Q 026702           85 MRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMV------TQLRDEAQKLKVSNE-----KLLGKINELKCEKNEL  153 (235)
Q Consensus        85 rRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yI------k~Lr~~vq~Lk~~n~-----~L~~ei~~Lk~EknEL  153 (235)
                      ...+.++..+..|+.-|.    .....---|.+-+.|+      .+++.++..|..++.     .++.+..+|..+.+.|
T Consensus       991 ~e~~~l~~~i~~l~kel~----~~~~~kr~l~dnL~~~~~~~~l~el~~eI~~l~~~~~~~~~~~~~~e~~~l~~~~~~l 1066 (1311)
T TIGR00606       991 KHQEKINEDMRLMRQDID----TQKIQERWLQDNLTLRKRENELKEVEEELKQHLKEMGQMQVLQMKQEHQKLEENIDLI 1066 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHH
Confidence            346677888888888882    2334445567888888      555555555555443     3444555566666666


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 026702          154 RDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       154 r~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ..++..+..++.+|+.|+..
T Consensus      1067 ~~~~a~l~g~~k~le~qi~~ 1086 (1311)
T TIGR00606      1067 KRNHVLALGRQKGYEKEIKH 1086 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            65555555666666665554

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

>TIGR01554 major_cap_HK97 phage major capsid protein, HK97 family

Probab=84.92  E-value=3.7  Score=38.46  Aligned_cols=58  Identities=22%  Similarity=0.245  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           87 RDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKC  148 (235)
Q Consensus        87 RdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~  148 (235)
                      |+++|+.=.+.++++.    .+..+..=+.+.-.-+++|+..+++++.+.+.+..+++++..
T Consensus         5 ~~~~~~~~~~~r~l~~----~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   62 (378)
T TIGR01554         5 KEQREEIVAEIRSLLD----KAEKLEKELTAAALEKEELETDVEKLKEEIKLLEDAIADLEK   62 (378)
T ss_pred             HHHHHHHHHHHHHHHh----hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6677777777777773    111111112222223345555555555555555444444433

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

>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=84.89  E-value=0.74  Score=36.39  Aligned_cols=47  Identities=28%  Similarity=0.511  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHH
Q 026702          117 DAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNE  163 (235)
Q Consensus       117 dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e  163 (235)
                      +.=+||..|..++..|..++..|..++++|..+..+++.....|+..
T Consensus        22 eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~~~   68 (131)
T PF05103_consen   22 EVDDFLDELAEELERLQRENAELKEEIEELQAQLEELREEEESLQRA   68 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT--------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHh
Confidence            34577777777777777777777666666655555555544444443

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.

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

Probab=84.85  E-value=7.1  Score=34.23  Aligned_cols=25  Identities=36%  Similarity=0.480  Sum_probs=11.0

Q ss_pred             HHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          149 EKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       149 EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      |+..|..+...++.+++..+.+++.
T Consensus       160 ei~~lks~~~~l~~~~~~~e~~F~~  184 (190)
T PF05266_consen  160 EISRLKSEAEALKEEIENAELEFQS  184 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444

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

Probab=84.79  E-value=5  Score=34.01  Aligned_cols=37  Identities=19%  Similarity=0.232  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHhHhHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLG---KINELKCEKNELRDEKQ  158 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~---ei~~Lk~EknELr~E~~  158 (235)
                      +..|+.++.....++..|..   .+++|+.++.+|+.++.
T Consensus        29 ~~~~k~ql~~~d~~i~~Lk~~~~d~eeLk~~i~~lq~~~~   68 (155)
T PF06810_consen   29 RDNLKTQLKEADKQIKDLKKSAKDNEELKKQIEELQAKNK   68 (155)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHH
Confidence            33444444444444444443   34444444444444443

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

>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=84.70  E-value=10  Score=31.99  Aligned_cols=78  Identities=26%  Similarity=0.378  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHH
Q 026702           87 RDRLNDRFMELASILDPGRPPKMDKTVLLADAVQ---MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNE  163 (235)
Q Consensus        87 RdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~---yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e  163 (235)
                      .+.|-+++..|-+=|.-   ...++..+.-+|=.   .|..|+.++..+-.+...|..+...|+.|+..|..+.+..+..
T Consensus        19 ~dsle~~v~~LEreLe~---~q~~~e~~~~daEn~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~k   95 (140)
T PF10473_consen   19 KDSLEDHVESLERELEM---SQENKECLILDAENSKAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKKQEK   95 (140)
T ss_pred             HhhHHHHHHHHHHHHHH---HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45566777777666622   34455555544422   2333444444444444444444444444444444443333333


Q ss_pred             HHHH
Q 026702          164 KENL  167 (235)
Q Consensus       164 ~e~L  167 (235)
                      ++.|
T Consensus        96 v~eL   99 (140)
T PF10473_consen   96 VSEL   99 (140)
T ss_pred             HHHH
Confidence            3333

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

>PRK04406 hypothetical protein; Provisional

Probab=84.68  E-value=6.3  Score=29.80  Aligned_cols=49  Identities=10%  Similarity=0.173  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le  168 (235)
                      ..|.+|+.++.-++..++.|...+-...+++..|+.+...|...+..++
T Consensus        11 ~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~~~   59 (75)
T PRK04406         11 ERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVKNMD   59 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            5788888888888888888888887778888888887777765554443

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

Probab=84.68  E-value=0.43  Score=49.54  Aligned_cols=80  Identities=18%  Similarity=0.179  Sum_probs=62.7

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHHhhcCCCC----CCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           74 SASGSKACREKMRRDRLNDRFMELASILDPGR----PPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCE  149 (235)
Q Consensus        74 ~~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~----~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~E  149 (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~  728 (856)
T KOG3582|consen  650 NRPITHISAEQKRRFNIKLQFDVLNSLS-SNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAHSLRKEISELNAV  728 (856)
T ss_pred             CCcccCccHHHHHHhhHHhhhHhhhhhc-cCcccccchhhhccccccCceeeeeccchhccccchhhhhhhhhhHHHHHH
Confidence            4688999999999999999999999888 432    24888888899999999988877777766666676666666666


Q ss_pred             HhHhH
Q 026702          150 KNELR  154 (235)
Q Consensus       150 knELr  154 (235)
                      ++-++
T Consensus       729 ~~~~~  733 (856)
T KOG3582|consen  729 ISACQ  733 (856)
T ss_pred             HHHhh
Confidence            65443

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

Probab=84.60  E-value=5.5  Score=41.95  Aligned_cols=45  Identities=20%  Similarity=0.393  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          131 KLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       131 ~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      .-.+..+.|.++...+|+...+++-++.+|..++|+|.++++.+-
T Consensus       213 aAle~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL~  257 (916)
T KOG0249|consen  213 AALEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQLR  257 (916)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            333455667788888888888888888888888888888877754

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

Probab=84.52  E-value=6.3  Score=31.75  Aligned_cols=69  Identities=22%  Similarity=0.228  Sum_probs=33.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHH
Q 026702           80 ACREKMRRDRLNDRFMELASILDPGRPPKMDKTVL-LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDE  156 (235)
Q Consensus        80 ~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasI-L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E  156 (235)
                      .+..++||..|.-....+-..+ -       ..++ +..-+.-+..|..+++.+++++++|..+...|++|++.|+++
T Consensus        17 ~~~~~~~~~~l~~~l~~~l~~f-~-------~~~~~g~~~~~~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg   86 (117)
T COG2919          17 GERRVRRRRILTLVLLALLALF-Q-------YLAWFGKNGAADVLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG   86 (117)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHH-H-------HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            4455555655555555554444 1       1111 111222233345555555666666665555555555555555

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

Probab=84.40  E-value=14  Score=27.74  Aligned_cols=35  Identities=14%  Similarity=0.315  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDE  156 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E  156 (235)
                      ++.|++.++++.+..+.+++++..+..|.+++-.+
T Consensus        21 l~~l~~~l~~~~~ti~~l~~~~~~i~~e~~~ll~~   55 (90)
T PF06103_consen   21 LKKLKKTLDEVNKTIDTLQEQVDPITKEINDLLHN   55 (90)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444443333

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

Probab=84.37  E-value=6.2  Score=29.02  Aligned_cols=51  Identities=16%  Similarity=0.178  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      +.|.+|+.++.-++..++.|...+-....++..|+.+...|...+..++..
T Consensus         4 ~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~~~   54 (69)
T PF04102_consen    4 ERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELEDP   54 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            456677777777777777777777777777777777777777777766643

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.

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

Probab=84.29  E-value=7.9  Score=29.94  Aligned_cols=55  Identities=31%  Similarity=0.425  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLG---KINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~---ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +.-+.+|+.+-..+..+...+..   +..+|+.+..++.++...|..+...++.++..
T Consensus        42 ~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~~e~~l~~   99 (108)
T PF02403_consen   42 QQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKELEEELNE   99 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455566666666665555443   46667777777777777777777777777766

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 ....

>KOG4797 consensus Transcriptional regulator [Transcription]

Probab=83.96  E-value=5  Score=33.09  Aligned_cols=32  Identities=28%  Similarity=0.300  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHH
Q 026702          132 LKVSNEKLLGKINELKCEKNELRDEKQRLKNE  163 (235)
Q Consensus       132 Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e  163 (235)
                      .+++.+.|+++|++|....+.|+.||..||.-
T Consensus        65 VREEVe~Lk~qI~eL~er~~~Le~EN~lLk~~   96 (123)
T KOG4797|consen   65 VREEVEVLKEQIRELEERNSALERENSLLKTL   96 (123)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            34556666677777777777788888777654

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

Probab=83.90  E-value=12  Score=32.92  Aligned_cols=47  Identities=28%  Similarity=0.359  Sum_probs=32.6

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHH
Q 026702          109 MDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDE  156 (235)
Q Consensus       109 ~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E  156 (235)
                      .||. .|..+=.-++.++.++..|+.+++.|......|..|+++|.+.
T Consensus        83 kdK~-~L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~~k  129 (201)
T PF13851_consen   83 KDKQ-SLQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQERDELYRK  129 (201)
T ss_pred             HHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444 4555666667777777777777777777777777777777654

>TIGR02209 ftsL_broad cell division protein FtsL

Probab=83.78  E-value=3.5  Score=30.43  Aligned_cols=33  Identities=36%  Similarity=0.449  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHH
Q 026702          123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRD  155 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~  155 (235)
                      .++..+++.++.+.+.++.+..+|+.|.+.|.+
T Consensus        27 ~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~   59 (85)
T TIGR02209        27 RQLNNELQKLQLEIDKLQKEWRDLQLEVAELSR   59 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            344455555555555555555555555555444

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.

>PRK02119 hypothetical protein; Provisional

Probab=83.71  E-value=9.3  Score=28.65  Aligned_cols=53  Identities=9%  Similarity=0.092  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          116 ADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       116 ~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            34446788888888888888888888888888888888888888876666554

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

Probab=83.63  E-value=25  Score=31.69  Aligned_cols=18  Identities=22%  Similarity=0.447  Sum_probs=7.3

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKL  139 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L  139 (235)
                      |.+|+..+..+..++..|
T Consensus        56 l~~lr~~id~~~~eka~l   73 (312)
T PF00038_consen   56 LRELRRQIDDLSKEKARL   73 (312)
T ss_dssp             HHCHHHHHHHHHHHHHHH
T ss_pred             HHHhHHhhhhHHHHhhHH
Confidence            344444444444333333

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 ....

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

Probab=83.59  E-value=11  Score=32.28  Aligned_cols=50  Identities=24%  Similarity=0.353  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      .-.++|+.+++.|+.+|..|+...+.+......|.+....|+.+...+..
T Consensus        89 ~e~k~L~~~v~~Le~e~r~L~~~~~~~~~q~~rlee~e~~l~~e~~~l~e  138 (158)
T PF09744_consen   89 QERKDLQSQVEQLEEENRQLELKLKNLSDQSSRLEEREAELKKEYNRLHE  138 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccccchhHHHHHHHHHHHHH
Confidence            34456777777777777776655555555555555555555555444443

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

>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=83.55  E-value=1.3  Score=32.56  Aligned_cols=29  Identities=24%  Similarity=0.400  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          141 GKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       141 ~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      +|++.||..+.+|.+.+..|+.|...|++
T Consensus        14 EEVevLK~~I~eL~~~n~~Le~EN~~Lk~   42 (59)
T PF01166_consen   14 EEVEVLKEQIAELEERNSQLEEENNLLKQ   42 (59)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44555555555555555555555555544

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.

>PRK14011 prefoldin subunit alpha; Provisional

Probab=83.51  E-value=7.9  Score=32.66  Aligned_cols=52  Identities=19%  Similarity=0.347  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      +.+|++|   ++.+++.|+...++|.+.+.++..+.++++.+.+   .....++++.+
T Consensus        86 ~~eA~~~---~~~ri~~l~~~~~~l~~~i~~~~~~~~~l~~~L~---~k~~~~~~~~~  137 (144)
T PRK14011         86 VSEVIED---FKKSVEELDKTKKEGNKKIEELNKEITKLRKELE---KRAQAIEQRQA  137 (144)
T ss_pred             HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHhh
Confidence            5778887   6678888888888888888888888888887643   33444544443

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

Probab=83.48  E-value=12  Score=31.84  Aligned_cols=12  Identities=33%  Similarity=0.354  Sum_probs=6.1

Q ss_pred             HHHHHHHHHhhc
Q 026702           90 LNDRFMELASIL  101 (235)
Q Consensus        90 lNd~F~~Lr~lL  101 (235)
                      +...|.+|+.=+
T Consensus        56 ~~a~~~eLr~el   67 (177)
T PF07798_consen   56 FKAAIAELRSEL   67 (177)
T ss_pred             HHHHHHHHHHHH
Confidence            344555555544

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

Probab=83.36  E-value=4.8  Score=35.04  Aligned_cols=14  Identities=29%  Similarity=0.586  Sum_probs=5.2

Q ss_pred             HHHHHHHHHHHHHH
Q 026702          159 RLKNEKENLERQVK  172 (235)
Q Consensus       159 ~Lk~e~e~Le~qlk  172 (235)
                      .|+.+++.|+.+|.
T Consensus       114 ~l~~~~~~l~~el~  127 (188)
T PF03962_consen  114 ELKKELKELKKELE  127 (188)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333333333333

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

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

Probab=83.33  E-value=0.82  Score=41.63  Aligned_cols=52  Identities=29%  Similarity=0.416  Sum_probs=43.3

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCC-CCCCCchhhhHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPG-RPPKMDKTVLLADAVQMVTQLR  126 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~-~~~K~dKasIL~dAI~yIk~Lr  126 (235)
                      ++.+=+.+||.|=-.||+-|..||.+||.. ..+|+.|...|.-|-.||-.|.
T Consensus        72 rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als  124 (254)
T KOG3898|consen   72 RRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALS  124 (254)
T ss_pred             hcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhc
Confidence            566668899999999999999999999533 2479999999988888887654

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

Probab=83.24  E-value=27  Score=29.52  Aligned_cols=81  Identities=21%  Similarity=0.426  Sum_probs=61.4

Q ss_pred             HHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702           89 RLNDRFMELASILDPGRPPKMDKTVLLADAVQMV-TQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus        89 klNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yI-k~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      .|++.|..|-.+++-+   . .....+.|+++-| .++...+...-.-...++.+++.++.|...|++.+.+++..+++|
T Consensus         5 el~~~~~~l~~~~e~~---~-~d~e~~~dtLe~i~~~~~~K~~~~~~~Ik~~ea~~e~~k~E~krL~~rkk~~e~~~~~L   80 (162)
T PF05565_consen    5 ELTDEYLELLELLEEG---D-LDEEAIADTLESIEDEIEEKADNIAKVIKNLEADIEAIKAEIKRLQERKKSIENRIDRL   80 (162)
T ss_pred             HHHHHHHHHHHHHhcC---C-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4788899999998532   2 4445667777663 345566666667777888889999999999999999999999998


Q ss_pred             HHHHHH
Q 026702          168 ERQVKA  173 (235)
Q Consensus       168 e~qlk~  173 (235)
                      ++-|..
T Consensus        81 k~yL~~   86 (162)
T PF05565_consen   81 KEYLLD   86 (162)
T ss_pred             HHHHHH
Confidence            886554

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

>TIGR01834 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit

Probab=83.08  E-value=5.8  Score=37.73  Aligned_cols=59  Identities=19%  Similarity=0.240  Sum_probs=39.3

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHH-HH----HHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          112 TVLLADAVQMVTQLRDEAQKLKVSN-EK----LLGKINELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       112 asIL~dAI~yIk~Lr~~vq~Lk~~n-~~----L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      +.|.++.|+-.-+|+.+.+++-+.. ..    .+.|+.++-+.+.|||.|..+|+.+++.|+.+
T Consensus       255 ak~~G~lvna~m~lr~~~qe~~e~~L~~LnlPTRsElDe~~krL~ELrR~vr~L~k~l~~l~~~  318 (320)
T TIGR01834       255 AKVHGKFINALMRLRIQQQEIVEALLKMLNLPTRSELDEAHQRIQQLRREVKSLKKRLGDLEAN  318 (320)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            4566677777777777766655433 22    45677777777777777777777777766643

This model represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. This model must be designated subfamily to indicate the heterogeneity of PHAs.

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=83.02  E-value=4.5  Score=38.37  Aligned_cols=49  Identities=27%  Similarity=0.433  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcCCC
Q 026702          123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQP  178 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~~~p  178 (235)
                      ..|++.+.+++..++.|+...       .+|..+...++.++++++.+++.+..+|
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~   52 (389)
T PRK03992          4 EALEERNSELEEQIRQLELKL-------RDLEAENEKLERELERLKSELEKLKSPP   52 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence            344455555555555544444       4444444455556666666777666655

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

Probab=82.96  E-value=8.6  Score=34.34  Aligned_cols=50  Identities=18%  Similarity=0.189  Sum_probs=27.4

Q ss_pred             HHHhhcCCCCCCCCchhhhH-------HHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           96 ELASILDPGRPPKMDKTVLL-------ADAV----QMVTQLRDEAQKLKVSNEKLLGKINEL  146 (235)
Q Consensus        96 ~Lr~lLpP~~~~K~dKasIL-------~dAI----~yIk~Lr~~vq~Lk~~n~~L~~ei~~L  146 (235)
                      .|.++|+-|- ...+|.++-       ++||    .|.+.|.++++...+....|.+.+...
T Consensus        47 vLQsLvDD~l-V~~eKIgtSnyywsfps~a~~~~ks~~qeLe~~L~~~~qk~~tl~e~~en~  107 (203)
T KOG3433|consen   47 VLQSLVDDGL-VIKEKIGTSNYYWSFPSEAICDRKSVLQELESQLATGSQKKATLGESIENR  107 (203)
T ss_pred             HHHHHhccch-HHHHHhcccccccccchHHHHHHHHHHHHHHHHHHHhhhhHhHHHHHHHHH
Confidence            4666664432 344454444       3443    466677777777666666666554333

>PRK04325 hypothetical protein; Provisional

Probab=82.89  E-value=6.8  Score=29.42  Aligned_cols=49  Identities=10%  Similarity=0.045  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            4588888888888888888888887788888888888777766655554

>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=82.89  E-value=7.3  Score=31.82  Aligned_cols=51  Identities=33%  Similarity=0.406  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      ++.++..++.+..+|..|-+..-.+..+..++|++...+..+...|+.++.
T Consensus        29 ~~~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~   79 (150)
T PF07200_consen   29 VQELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQ   79 (150)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555555555555555555444555555555555555555555555443

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.

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

Probab=82.81  E-value=27  Score=30.21  Aligned_cols=59  Identities=24%  Similarity=0.387  Sum_probs=31.9

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          111 KTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       111 KasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      .-.+-..|+.-+.+++.++..|+.....+...+..|+..+.+|+.....++.+++-|..
T Consensus        82 ~edLAr~al~~k~~~e~~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl~e~k~k~~~l~a  140 (221)
T PF04012_consen   82 REDLAREALQRKADLEEQAERLEQQLDQAEAQVEKLKEQLEELEAKLEELKSKREELKA  140 (221)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455566666666666666666665555555444444444444444444444444433

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

>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=82.73  E-value=15  Score=27.61  Aligned_cols=54  Identities=13%  Similarity=0.199  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          116 ADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       116 ~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      .+.-+-++++++.++.++++.+.+..|+..+-.+.|++-++...-....+.+-+
T Consensus        22 ~~l~~~l~~~~~ti~~l~~~~~~i~~e~~~ll~~~n~l~~dv~~k~~~v~~~~~   75 (90)
T PF06103_consen   22 KKLKKTLDEVNKTIDTLQEQVDPITKEINDLLHNTNELLEDVNEKLEKVDPVFE   75 (90)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            334455666666666666666666666666666666666654444444443333

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=82.69  E-value=6.9  Score=33.05  Aligned_cols=30  Identities=40%  Similarity=0.629  Sum_probs=17.6

Q ss_pred             HHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          144 NELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       144 ~~Lk~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            455556666666666666666665555554

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

Probab=82.60  E-value=8.9  Score=38.95  Aligned_cols=30  Identities=27%  Similarity=0.478  Sum_probs=12.9

Q ss_pred             HHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          144 NELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       144 ~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ..|+.|++.|..++..++..+..|+..++.
T Consensus       202 e~l~~E~~~L~~q~~e~~~ri~~LEedi~~  231 (546)
T PF07888_consen  202 EELKEERESLKEQLAEARQRIRELEEDIKT  231 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444443

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 [].

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=82.60  E-value=4.7  Score=38.27  Aligned_cols=44  Identities=20%  Similarity=0.337  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKN  162 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~  162 (235)
                      ..++++|+.++++|+..+..|..+.+.++.+..++++++..|+.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   50 (389)
T PRK03992          7 EERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKS   50 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            45667788899999999999988888888777777776655543

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

Probab=82.52  E-value=7.2  Score=37.77  Aligned_cols=53  Identities=21%  Similarity=0.257  Sum_probs=39.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Q 026702          114 LLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKEN  166 (235)
Q Consensus       114 IL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~  166 (235)
                      ++.++=..+..|++-+..++++|..|+....++.+|..|..+|.+.|-.|...
T Consensus       121 vf~k~k~~~q~LE~li~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE  173 (401)
T PF06785_consen  121 VFMKTKGDIQHLEGLIRHLREENQCLQLQLDALQQECGEKEEESQTLNRELAE  173 (401)
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHH
Confidence            45555566677788888888888888888888888888888887777555544

>PF14988 DUF4515: Domain of unknown function (DUF4515)

Probab=82.48  E-value=10  Score=33.58  Aligned_cols=47  Identities=23%  Similarity=0.396  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      .|-.....+..+|..|+.++..|-.+...|+..+..|..++..|.++
T Consensus       153 ~l~e~~~~i~~EN~~L~k~L~~l~~e~~~L~~~~~~Le~qk~~L~~e  199 (206)
T PF14988_consen  153 SLDEFTRSIKRENQQLRKELLQLIQEAQKLEARKSQLEKQKQQLQQE  199 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555555555555555555555555555555555555544

>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]

Probab=82.45  E-value=12  Score=37.98  Aligned_cols=36  Identities=31%  Similarity=0.361  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEK  157 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~  157 (235)
                      +.++++++.+|..++..++.+++++..|++||..=.
T Consensus       228 l~~q~Ee~skLlsql~d~qkk~k~~~~Ekeel~~~L  263 (596)
T KOG4360|consen  228 LSRQQEENSKLLSQLVDLQKKIKYLRHEKEELDEHL  263 (596)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence            334445555566666666777777777777654433

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

Probab=82.38  E-value=29  Score=29.91  Aligned_cols=40  Identities=23%  Similarity=0.244  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRL  160 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~L  160 (235)
                      -+.+++.+++.|+.+...|.+.|+.+-.++.+.+.+...+
T Consensus        23 ~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~   62 (188)
T PF10018_consen   23 EHQENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTL   62 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3355666777777777777777777777777777766544

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

>COG3937 Uncharacterized conserved protein [Function unknown]

Probab=82.36  E-value=9.3  Score=31.21  Aligned_cols=58  Identities=26%  Similarity=0.374  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH--------hHhHHHHHHHHHHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNE-KLLGKINELKCEK--------NELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~-~L~~ei~~Lk~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            46788888888888775444332 2333344333332        4666666677777777766654

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

Probab=82.31  E-value=11  Score=27.17  Aligned_cols=21  Identities=33%  Similarity=0.559  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q 026702          154 RDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       154 r~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      ++....+..++++|+..|..+
T Consensus        45 r~kl~~~~~~~~~l~~~l~~L   65 (66)
T PF10458_consen   45 REKLEELEEELEKLEEALEQL   65 (66)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHHHhc
Confidence            334556777777777777654

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.

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

Probab=82.27  E-value=17  Score=35.25  Aligned_cols=90  Identities=21%  Similarity=0.267  Sum_probs=56.5

Q ss_pred             HHHHHHHHHHHhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HhHhHHHHHHH
Q 026702           88 DRLNDRFMELASILDPGR--PPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCE-----KNELRDEKQRL  160 (235)
Q Consensus        88 dklNd~F~~Lr~lLpP~~--~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~E-----knELr~E~~~L  160 (235)
                      +.|-++|.+|..+| -+.  .+..++..-|+.-..+|..+-....++++..+.|..--.-|..+     +...++|...|
T Consensus        10 ~~~~~r~~el~~~L-~~p~v~~d~~~~~~lske~a~l~~iv~~~~~~~~~~~~l~~a~~~l~~~~D~em~ema~~Ei~~~   88 (363)
T COG0216          10 ESLLERYEELEALL-SDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDAKEMLAEEKDPEMREMAEEEIKEL   88 (363)
T ss_pred             HHHHHHHHHHHHHh-cCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHH
Confidence            45677999999888 321  13445666666666666655555555555444443322222211     13467788899


Q ss_pred             HHHHHHHHHHHHHhcCCC
Q 026702          161 KNEKENLERQVKALSSQP  178 (235)
Q Consensus       161 k~e~e~Le~qlk~~~~~p  178 (235)
                      +.+++.|+.+|+.+=.|+
T Consensus        89 ~~~~~~le~~L~~lLlPk  106 (363)
T COG0216          89 EAKIEELEEELKILLLPK  106 (363)
T ss_pred             HHHHHHHHHHHHHhcCCC
Confidence            999999999999976655

>KOG0979 consensus Structural maintenance of chromosome protein SMC5/Spr18, SMC superfamily [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=82.14  E-value=9.2  Score=41.44  Aligned_cols=83  Identities=23%  Similarity=0.260  Sum_probs=57.7

Q ss_pred             CchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHH
Q 026702           77 GSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDE  156 (235)
Q Consensus        77 ~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E  156 (235)
                      .+-...+..++.++=+.+..|++.+.- +.             .-++.|++++++...+++.++.++..++++..++..+
T Consensus       621 ~~~~~~l~~~~~~~ee~~~~~~~~~~~-~~-------------~~~r~lee~~~k~~k~le~~~~~~~~~~~er~~~~~~  686 (1072)
T KOG0979|consen  621 FSVSPVLEELDNRIEEEIQKLKAEIDI-RS-------------STLRELEEKKQKERKELEEEQKKLKLLKRERTKLNSE  686 (1072)
T ss_pred             hccchHHHHHHHHHHHHHHHHHHHHhh-hh-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            334556777777888888888888832 11             3456677777777777777777777777777777777


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 026702          157 KQRLKNEKENLERQVKA  173 (235)
Q Consensus       157 ~~~Lk~e~e~Le~qlk~  173 (235)
                      ...++..++++|.++..
T Consensus       687 ~~~~~~r~~~ie~~~~~  703 (1072)
T KOG0979|consen  687 LKSYQQRKERIENLVVD  703 (1072)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            66666666666665443

>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=82.10  E-value=12  Score=34.70  Aligned_cols=56  Identities=25%  Similarity=0.306  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHH-------HHHHHHHHHHHH
Q 026702          118 AVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLK-------NEKENLERQVKA  173 (235)
Q Consensus       118 AI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk-------~e~e~Le~qlk~  173 (235)
                      +-.-|.+++..+..+..+...|..+|+.-+.|.+-.+.....|+       .|-|+||.+|+.
T Consensus       174 ~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~vRPAfmdEyEklE~EL~~  236 (267)
T PF10234_consen  174 VQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERNQKRLQSLQSVRPAFMDEYEKLEEELQK  236 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHH
Confidence            33444455555555555666677777777777666666655444       477777777765

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 [].

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

Probab=81.91  E-value=6  Score=31.12  Aligned_cols=20  Identities=35%  Similarity=0.659  Sum_probs=7.8

Q ss_pred             HHHHHHHHhHhHHHHHHHHH
Q 026702          143 INELKCEKNELRDEKQRLKN  162 (235)
Q Consensus       143 i~~Lk~EknELr~E~~~Lk~  162 (235)
                      +++|..+++.|.+|+..|+.
T Consensus        51 v~~L~~e~~~l~~E~e~L~~   70 (87)
T PF12709_consen   51 VDELENENKALKRENEQLKK   70 (87)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            33334444443333333333

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 [].

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

Probab=81.86  E-value=1.8  Score=37.45  Aligned_cols=40  Identities=28%  Similarity=0.323  Sum_probs=17.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Q 026702          114 LLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEK  157 (235)
Q Consensus       114 IL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~  157 (235)
                      -|..||+.---|+.++    +|.+.|+.++..||.|..+|+.|.
T Consensus         8 klN~AIERnalLE~EL----dEKE~L~~~~QRLkDE~RDLKqEl   47 (166)
T PF04880_consen    8 KLNQAIERNALLESEL----DEKENLREEVQRLKDELRDLKQEL   47 (166)
T ss_dssp             HHHHHHHHHHHHHHHH----HHHHHHHHCH--------------
T ss_pred             HHHHHHHHhHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4677888888888777    334455555555555555444444

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.

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

Probab=81.84  E-value=40  Score=37.54  Aligned_cols=9  Identities=11%  Similarity=0.021  Sum_probs=4.5

Q ss_pred             CCCCCcccC
Q 026702           29 LDPPEVLWS   37 (235)
Q Consensus        29 ~~~~~f~w~   37 (235)
                      .|+=||.+.
T Consensus       395 LPFIGfTy~  403 (1317)
T KOG0612|consen  395 LPFIGFTYT  403 (1317)
T ss_pred             CCeeeeeec
Confidence            344455554

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

Probab=81.84  E-value=7.2  Score=39.97  Aligned_cols=56  Identities=21%  Similarity=0.273  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            59999999999999999999999999999999999999999999999999887743

>TIGR01069 mutS2 MutS2 family protein

Probab=81.84  E-value=8.6  Score=40.22  Aligned_cols=12  Identities=8%  Similarity=0.288  Sum_probs=5.6

Q ss_pred             hHHHHHHHHHHH
Q 026702          114 LLADAVQMVTQL  125 (235)
Q Consensus       114 IL~dAI~yIk~L  125 (235)
                      ||.+|-+++.+.
T Consensus       498 ii~~A~~~~~~~  509 (771)
T TIGR01069       498 IIEQAKTFYGEF  509 (771)
T ss_pred             HHHHHHHHHHhh
Confidence            445554444433

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.

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

Probab=81.77  E-value=13  Score=37.58  Aligned_cols=71  Identities=20%  Similarity=0.226  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHH
Q 026702           84 KMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRD  155 (235)
Q Consensus        84 RrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~  155 (235)
                      --=+..||+.|..|..+. -.-....-|.+||+.|=....++...-..|+........+|...-.++|.|-+
T Consensus       107 ~sl~~~L~~ff~s~q~la-~~P~~~a~r~~vl~~a~~l~~~in~~~~~L~~l~~~i~~~I~~~V~~vNsLl~  177 (552)
T COG1256         107 SSLSTLLNDFFNSLQELA-SNPSDTAARQAVLSKAQTLVNQINNTYEQLTDLRKDINAEIAATVDEVNSLLK  177 (552)
T ss_pred             ccHHHHHHHHHHHHHHHH-hCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            444677888888888887 32223567778888887776666655555555444444444433344444333

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

Probab=81.76  E-value=9.8  Score=34.78  Aligned_cols=53  Identities=17%  Similarity=0.276  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      ..+++.++.+...+......++.+.++|+.++..+..+.+.+...+++++.++
T Consensus        30 ~~~l~k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e~kl   82 (239)
T COG1579          30 RKALKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKL   82 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555555555666666666666666666666666655555

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

Probab=81.74  E-value=7  Score=26.81  Aligned_cols=19  Identities=47%  Similarity=0.576  Sum_probs=9.0

Q ss_pred             hHhHHHHHHHHHHHHHHHH
Q 026702          151 NELRDEKQRLKNEKENLER  169 (235)
Q Consensus       151 nELr~E~~~Lk~e~e~Le~  169 (235)
                      ..|+.++..||-++.++.+
T Consensus        30 ~~LKk~kL~LKDei~~ll~   48 (49)
T PF04325_consen   30 ERLKKEKLRLKDEIYRLLR   48 (49)
T ss_dssp             HHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHHc
Confidence            3444445555555555443

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

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

Probab=81.71  E-value=6  Score=40.32  Aligned_cols=28  Identities=21%  Similarity=0.565  Sum_probs=17.1

Q ss_pred             HHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          143 INELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       143 i~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      ++.+..|+++|..+...+..++++|.+.
T Consensus       334 ve~mn~Er~~l~r~l~~i~~~~d~l~k~  361 (581)
T KOG0995|consen  334 VERMNLERNKLKRELNKIQSELDRLSKE  361 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445556666666666666666666653

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

Probab=81.57  E-value=9.8  Score=38.66  Aligned_cols=12  Identities=33%  Similarity=0.473  Sum_probs=4.9

Q ss_pred             HHHHHHHHHhhc
Q 026702           90 LNDRFMELASIL  101 (235)
Q Consensus        90 lNd~F~~Lr~lL  101 (235)
                      +.+-+.+|+..+
T Consensus       118 l~~e~~elr~~~  129 (546)
T KOG0977|consen  118 LREELKELRKKL  129 (546)
T ss_pred             hHHHHHHHHHHH
Confidence            334444444443

>PRK10869 recombination and repair protein; Provisional

Probab=81.51  E-value=15  Score=36.81  Aligned_cols=87  Identities=21%  Similarity=0.184  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHhHhHHHHHHHH
Q 026702           85 MRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKV---SNEKLLGKINELKCEKNELRDEKQRLK  161 (235)
Q Consensus        85 rRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~---~n~~L~~ei~~Lk~EknELr~E~~~Lk  161 (235)
                      .|=+.|++|+..|..+-   +  |-.  .-+.+.+.|..+++.+++.|+.   ..+.|+.+++.++.+..++..+.+..+
T Consensus       296 ~~l~~ie~Rl~~l~~L~---r--Kyg--~~~~~~~~~~~~l~~eL~~L~~~e~~l~~Le~e~~~l~~~l~~~A~~LS~~R  368 (553)
T PRK10869        296 NRLAELEQRLSKQISLA---R--KHH--VSPEELPQHHQQLLEEQQQLDDQEDDLETLALAVEKHHQQALETAQKLHQSR  368 (553)
T ss_pred             HHHHHHHHHHHHHHHHH---H--HhC--CCHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34578888888888887   3  322  2588999999999999888775   567788888888888888777776555


Q ss_pred             HH-HH----HHHHHHHHhcCCC
Q 026702          162 NE-KE----NLERQVKALSSQP  178 (235)
Q Consensus       162 ~e-~e----~Le~qlk~~~~~p  178 (235)
                      .+ -+    .+..+|+.++.+-
T Consensus       369 ~~aA~~l~~~v~~~L~~L~m~~  390 (553)
T PRK10869        369 QRYAKELAQLITESMHELSMPH  390 (553)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCC
Confidence            54 23    3455666666544

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

Probab=81.44  E-value=9.1  Score=31.95  Aligned_cols=15  Identities=27%  Similarity=0.277  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHHHHHH
Q 026702          127 DEAQKLKVSNEKLLG  141 (235)
Q Consensus       127 ~~vq~Lk~~n~~L~~  141 (235)
                      ..++.|+.+++++++
T Consensus        42 ~K~~~lE~eld~~~~   56 (143)
T PF12718_consen   42 KKNQQLEEELDKLEE   56 (143)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            333333333333333

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 [].

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

Probab=81.44  E-value=2  Score=32.95  Aligned_cols=25  Identities=32%  Similarity=0.557  Sum_probs=15.1

Q ss_pred             hHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          151 NELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       151 nELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      ++|++|+.+||.++.+|+.+|+.+.
T Consensus         3 ~ei~eEn~~Lk~eiqkle~ELq~~~   27 (76)
T PF07334_consen    3 HEIQEENARLKEEIQKLEAELQQNK   27 (76)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666666666666666665543

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

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=81.37  E-value=1.7  Score=43.06  Aligned_cols=43  Identities=23%  Similarity=0.394  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCCC--CCCCchhhhHHHHHHHHHH
Q 026702           82 REKMRRDRLNDRFMELASILDPGR--PPKMDKTVLLADAVQMVTQ  124 (235)
Q Consensus        82 ~ERrRRdklNd~F~~Lr~lLpP~~--~~K~dKasIL~dAI~yIk~  124 (235)
                      .-|.||++=|--|.+|..+||--+  ....||++|+.=|..|||-
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKm   52 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKM   52 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHH
Confidence            668999999999999999994321  2469999999999999983

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

Probab=81.32  E-value=2.5  Score=39.33  Aligned_cols=52  Identities=25%  Similarity=0.264  Sum_probs=41.6

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCC-CCCCCchhhhHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPG-RPPKMDKTVLLADAVQMVTQLR  126 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~-~~~K~dKasIL~dAI~yIk~Lr  126 (235)
                      ++..-+.+||+|=..||..|..|+.++|-+ ...|.+|-..|.-|-.||.-|-
T Consensus       174 rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~  226 (285)
T KOG4395|consen  174 RRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALG  226 (285)
T ss_pred             hhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhH
Confidence            455567899999999999999999999432 2358889888888888877553

>PF14282 FlxA: FlxA-like protein

Probab=81.27  E-value=7.2  Score=30.94  Aligned_cols=60  Identities=17%  Similarity=0.286  Sum_probs=38.5

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          112 TVLLADAVQMVTQLRDEAQKLKV----SNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       112 asIL~dAI~yIk~Lr~~vq~Lk~----~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      .+.+..--+-|+.|+.+++.|..    ..+.-+..++.|..++..|+.....|..++..-..+-
T Consensus        18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~~~~~~~~   81 (106)
T PF14282_consen   18 DSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQAEQQQQK   81 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45555555667777777777776    2244556667777777777777777766665554443

>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids []

Probab=81.26  E-value=11  Score=28.29  Aligned_cols=56  Identities=27%  Similarity=0.299  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHHHHH----HHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcCCC
Q 026702          123 TQLRDEAQKLKVSNE----KLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQP  178 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~----~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~~~p  178 (235)
                      ++|....+.|++...    ..+.....|.......+.++..|..++..|.+|+..++..+
T Consensus         6 ~qLl~ale~Lq~~y~~q~~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql   65 (70)
T PF04899_consen    6 KQLLSALEELQQSYEKQQQEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLSEQL   65 (70)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345555555555443    34445666777777777778888888888888888876543

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

Probab=81.25  E-value=12  Score=27.16  Aligned_cols=47  Identities=21%  Similarity=0.348  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          127 DEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       127 ~~vq~Lk~~n~~L~~ei~~Lk~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            45677777888888888888888888888888777777766655543

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.

>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]

Probab=81.23  E-value=9.3  Score=35.90  Aligned_cols=55  Identities=20%  Similarity=0.267  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINE----LKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~----Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      |.++-...++|+..+++|..+.+.+.++.+.    --++...|+++++.+++.+|.|+.
T Consensus        54 L~q~etrnrdl~t~nqrl~~E~e~~Kek~e~q~~q~y~q~s~Leddlsqt~aikeql~k  112 (333)
T KOG1853|consen   54 LDQLETRNRDLETRNQRLTTEQERNKEKQEDQRVQFYQQESQLEDDLSQTHAIKEQLRK  112 (333)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444455555555555555555444433211    123345677777777777776554

>KOG0982 consensus Centrosomal protein Nuf [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=81.16  E-value=7.7  Score=38.60  Aligned_cols=45  Identities=31%  Similarity=0.330  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          127 DEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       127 ~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      .++|.|+.+|..|+..+..|+...++|-.|++++-.++|-|..|+
T Consensus       304 mr~qqleeentelRs~~arlksl~dklaee~qr~sd~LE~lrlql  348 (502)
T KOG0982|consen  304 MRDQQLEEENTELRSLIARLKSLADKLAEEDQRSSDLLEALRLQL  348 (502)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHH
Confidence            334555555555555555555555555555555555555444443

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=81.11  E-value=17  Score=37.72  Aligned_cols=48  Identities=23%  Similarity=0.297  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      ..+.+++.+++.++..+..++.++..|+.+.+.++.+...++.+++.|
T Consensus       440 ~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~l  487 (1179)
T TIGR02168       440 AELEELEEELEELQEELERLEEALEELREELEEAEQALDAAERELAQL  487 (1179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444444444444444444444433

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.

>PF13747 DUF4164: Domain of unknown function (DUF4164)

Probab=81.07  E-value=9.6  Score=29.58  Aligned_cols=16  Identities=19%  Similarity=0.302  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSN  136 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n  136 (235)
                      +++.|...+..|+...
T Consensus         9 al~rL~~aid~LE~~v   24 (89)
T PF13747_consen    9 ALTRLEAAIDRLEKAV   24 (89)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3444555555555433

>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits

Probab=81.02  E-value=6.9  Score=30.41  Aligned_cols=42  Identities=26%  Similarity=0.439  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQR  159 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~  159 (235)
                      +.+|++|   |..++..|+...+.|..+++.++.+.+.+++..++
T Consensus        75 ~~eA~~~---l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~~  116 (120)
T PF02996_consen   75 LEEAIEF---LKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQQ  116 (120)
T ss_dssp             HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHH
T ss_pred             HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6788887   44566666666666666666555555555544433

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

>PRK05431 seryl-tRNA synthetase; Provisional

Probab=80.92  E-value=8.8  Score=37.22  Aligned_cols=51  Identities=27%  Similarity=0.442  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH----------HHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          123 TQLRDEAQKLKVSNEKLLGKIN----------ELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L~~ei~----------~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ++|+.+++.|+.+...+..+|+          +|+.+..+|+++...|+.+...++.++..
T Consensus        38 r~l~~~~~~lr~~rn~~sk~i~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~   98 (425)
T PRK05431         38 RELQTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKELKEEIKALEAELDELEAELEE   98 (425)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444455555554444444443          34444444555555555555555555554

>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=80.89  E-value=15  Score=33.26  Aligned_cols=61  Identities=21%  Similarity=0.298  Sum_probs=31.9

Q ss_pred             hhHHHHHHHHHHHHHH----HHHH---HHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          113 VLLADAVQMVTQLRDE----AQKL---KVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       113 sIL~dAI~yIk~Lr~~----vq~L---k~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      -.|.+-..-+..|..+    +++|   .+....|...|+.++.|++..++...++..|..+|..++..
T Consensus        32 ~~L~e~~kE~~~L~~Er~~h~eeLrqI~~DIn~lE~iIkqa~~er~~~~~~i~r~~eey~~Lk~~in~   99 (230)
T PF10146_consen   32 KCLEEYRKEMEELLQERMAHVEELRQINQDINTLENIIKQAESERNKRQEKIQRLYEEYKPLKDEINE   99 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555555544    2233   22334455556666666665555555555555555555444

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.

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

Probab=80.80  E-value=9.2  Score=30.79  Aligned_cols=56  Identities=16%  Similarity=0.132  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      |.-..-|+..+---....-..+..++.++..+++|...|..++..|++|+++|+..
T Consensus        31 l~~~l~~f~~~~~~g~~~~~~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg   86 (117)
T COG2919          31 LLALLALFQYLAWFGKNGAADVLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG   86 (117)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            33344455444444455555666666666677777777777777777777777776

>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp

Probab=80.79  E-value=9.3  Score=36.06  Aligned_cols=13  Identities=15%  Similarity=0.455  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHHhc
Q 026702          163 EKENLERQVKALS  175 (235)
Q Consensus       163 e~e~Le~qlk~~~  175 (235)
                      |..|||..|+.|.
T Consensus       157 QN~KLEsLLqsME  169 (305)
T PF15290_consen  157 QNKKLESLLQSME  169 (305)
T ss_pred             hHhHHHHHHHHHH
Confidence            4455777777764

>PF05837 CENP-H: Centromere protein H (CENP-H); InterPro: IPR008426 Chromosome segregation in eukaryotes requires the kinetochore, a multi-protein structure that assembles on centromeric DNA, and which acts to link chromosomes to spindle microtubules

Probab=80.72  E-value=15  Score=29.16  Aligned_cols=53  Identities=23%  Similarity=0.409  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +-|.+++.+.-.++..|..|-.++.+|+.+...-+. ...+..++++++..++.
T Consensus        17 ~~L~~v~~~~l~l~~~n~el~~el~~l~~~~~~~~~-~~~~~~~l~~~~~~lk~   69 (106)
T PF05837_consen   17 EKLSDVEKKRLRLKRRNQELAQELLELAEKQKSQRE-DEELSEKLEKLEKELKK   69 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcc-chHHHHHHHHHHHHHHH
Confidence            444444555555555666666666666665544333 44566677777776665

Kinetochore structure and composition is highly conserved among vertebrates. The inner kinetochore is essential for kinetochore assembly, and is involved in chromosome segregation via regulation of the spindle. Inner kinetochore components include the multi-subunit CENP-H/I complex, which may function, in part, in directing centromere protein A (CENP-A) deposition to centromeres, where CENP-A is a centromere-specific histone H3 variant required for the organisation of centromeric chromatin during interphase. The CENP-H/I complex contains three functional classes of proteins [, ]: CENP-H class (includes CENP-H, -I, -K, -L) CENP-M class (includes CENP-M) CENP-O class (includes CENP-O, -P, -Q, -R, -50) CENP-H is required for the localisation of CENP-C, but not CENP-A, to the centromere. However, it may be involved in the incorporation of newly synthesised CENP-A into centromeres via its interaction with the CENP-A/CENP-HI complex. CENP-H contains a coiled-coil structure and a nuclear localisation signal. CENP-H is specifically and constitutively localised in kinetochores throughout the cell cycle, and may play a role in kinetochore organisation and function throughout the cell cycle []. Studies show that CENP-H may be associated with certain human cancers [, ]. This entry also includes Kinetochore protein Fta3 which is a subunit of the Sim4 complex. This complex is required for loading the DASH complex onto the kinetochore via interaction with dad1. Fta2, Fta3 and Fta4 associate with the central core and inner repeat region of the centromere [].; GO: 0043515 kinetochore binding, 0007059 chromosome segregation, 0051301 cell division, 0000777 condensed chromosome kinetochore, 0005634 nucleus

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=80.66  E-value=23  Score=35.81  Aligned_cols=65  Identities=17%  Similarity=0.265  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHH
Q 026702           87 RDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDE  156 (235)
Q Consensus        87 RdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E  156 (235)
                      ..++-+.+.+|..-| -    ..+.-.-+..-.+.+++++.++.+++.+...++.+++.++.++.+++.+
T Consensus       400 ~~~~e~el~~l~~~l-~----~~~~~e~i~~l~e~l~~l~~~l~~~~~~~~~~~~~~~~~~~~i~~~~~~  464 (650)
T TIGR03185       400 LRELEEELAEVDKKI-S----TIPSEEQIAQLLEELGEAQNELFRSEAEIEELLRQLETLKEAIEALRKT  464 (650)
T ss_pred             HHHHHHHHHHHHHHH-h----cCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445555555555 1    1111123444445555555555555555555555555555554444443

This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.

>PRK03947 prefoldin subunit alpha; Reviewed

Probab=80.61  E-value=25  Score=28.47  Aligned_cols=44  Identities=18%  Similarity=0.266  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          126 RDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       126 r~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      .+.+.-|+...+.|...++.|..+..+++++...+...+.++.+
T Consensus        93 ~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~l~~  136 (140)
T PRK03947         93 DEAIEILDKRKEELEKALEKLEEALQKLASRIAQLAQELQQLQQ  136 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444444444444433

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

Probab=80.53  E-value=7.6  Score=39.44  Aligned_cols=36  Identities=36%  Similarity=0.458  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          139 LLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       139 L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      |+.++..+++.+.-|.+|+..|+.|+.+|..+|+.+
T Consensus       153 leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~  188 (546)
T KOG0977|consen  153 LEAEINTLKRRIKALEDELKRLKAENSRLREELARA  188 (546)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH
Confidence            344556666667777777778888888877777653

>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=80.52  E-value=9.2  Score=28.07  Aligned_cols=43  Identities=14%  Similarity=0.230  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          131 KLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       131 ~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .+..++.+.+.....+.....+-...+..|..++++|+.+++.
T Consensus        15 ~~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee   57 (61)
T PF08826_consen   15 AIQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEMEE   57 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555566666666777777777666654

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

>KOG3156 consensus Uncharacterized membrane protein [Function unknown]

Probab=80.28  E-value=8.7  Score=34.85  Aligned_cols=43  Identities=28%  Similarity=0.413  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHH-HHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          131 KLKVSNEKLLGKINE-LKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       131 ~Lk~~n~~L~~ei~~-Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +++....+++.++.. .+.|-..||.|+.+|+.|+|+++++|..
T Consensus        98 QQ~~~f~kiRsel~S~e~sEF~~lr~e~EklkndlEk~ks~lr~  141 (220)
T KOG3156|consen   98 QQKVDFAKIRSELVSIERSEFANLRAENEKLKNDLEKLKSSLRH  141 (220)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445556555433 3455567999999999999999998875

>PRK02224 chromosome segregation protein; Provisional

Probab=80.26  E-value=19  Score=37.19  Aligned_cols=22  Identities=18%  Similarity=0.383  Sum_probs=9.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSN  136 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n  136 (235)
                      |.++.+-+..|++++..|+...
T Consensus       532 le~~~~~~~~l~~e~~~l~~~~  553 (880)
T PRK02224        532 IEEKRERAEELRERAAELEAEA  553 (880)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444333

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

Probab=80.07  E-value=6.5  Score=35.51  Aligned_cols=37  Identities=22%  Similarity=0.254  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHH
Q 026702          129 AQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKE  165 (235)
Q Consensus       129 vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e  165 (235)
                      .+.++..+..|+.+++++..|.+.|-+|.+.|+.+++
T Consensus       174 Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~  210 (216)
T KOG1962|consen  174 LEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIE  210 (216)
T ss_pred             HHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHh
Confidence            3334445566666677777777777777777766665

---

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_A	88	C-MYC, MYC proto-oncogene protein; transcription,	7e-12
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	5e-11
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	5e-11
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	4e-08
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	4e-07
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	3e-06
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	4e-05
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	8e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	8e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-04
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	2e-04
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	2e-04
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	5e-04

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

 Score = 58.9 bits (143), Expect = 7e-12
 Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 83  EKMRRDRLNDRFMELASIL-DPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLG 141
           E+ RR+ L   F  L   + +     K  K V+L  A   +  ++ E QKL    + L  
Sbjct: 14  ERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK 73

Query: 142 KINELKCEKNELR 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 = 56.2 bits (136), Expect = 5e-11
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 83  EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
           EK  R  +ND+ +EL  ++  G   K++K+ +L  A+  +  L+   QKLK  N  L   
Sbjct: 14  EKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA 72

Query: 143 INELK 147
           +++ K
Sbjct: 73  VHKSK 77

>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 = 56.2 bits (136), Expect = 5e-11
 Identities = 14/72 (19%), Positives = 29/72 (40%)

Query: 83  EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK 142
           E+ RRD + D F  L   +   +  K  +  +L  A + +  +R +    +   + L  +
Sbjct: 10  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ 69

Query: 143 INELKCEKNELR 154
              L+ +   L 
Sbjct: 70  NALLEQQVRALG 81

>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 = 48.5 bits (116), Expect = 4e-08
 Identities = 12/57 (21%), Positives = 24/57 (42%)

Query: 83  EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKL 139
           E+ RRD + D F  L   +   +  K  +  +L  A + +  +R +    +   + L
Sbjct: 20  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL 76

>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 = 45.4 bits (108), Expect = 4e-07
 Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 4/53 (7%)

Query: 83  EKMRRDRLNDRFMELASIL----DPGRPPKMDKTVLLADAVQMVTQLRDEAQK 131
           E+ RRD++N+  ++L+ I+             K  +L+ 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 = 43.3 bits (102), Expect = 3e-06
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 8/79 (10%)

Query: 83  EKMRRDRLNDRFMELASIL-DPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLG 141
           EK RR  L     +L  ++       +     LL  A   + +L D        + K + 
Sbjct: 9   EKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDS-------DRKAVH 61

Query: 142 KINELKCEKNELRDEKQRL 160
           +I++L+ E+  L+ + ++L
Sbjct: 62  QIDQLQREQRHLKRQLEKL 80

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens} Length = 168

 Score = 42.0 bits (98), Expect = 4e-05
 Identities = 14/63 (22%), Positives = 32/63 (50%)

Query: 115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
           L +A  ++    D A +L+ S+ ++   I++L+    EL++  + L+N K   ++    L
Sbjct: 15  LEEANDLLRTESDTAVRLRKSHTEMSKSISQLESLNRELQERNRILENSKSQTDKDYYQL 74

Query: 175 SSQ 177
            + 
Sbjct: 75  QAI 77

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli} Length = 81

 Score = 39.2 bits (91), Expect = 8e-05
 Identities = 15/57 (26%), Positives = 31/57 (54%)

Query: 118 AVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
           A+  +T L+ E ++LK  N  L  ++   + ++ EL  E   LK ++   + +++AL
Sbjct: 18  AIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQAL 74

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.1 bits (98), Expect = 1e-04
 Identities = 26/176 (14%), Positives = 50/176 (28%), Gaps = 51/176 (28%)

Query: 35  LWSSSTSNPPLSAEFNDSFGNLDAFKETGSRKRVRSGSCSASGSKACREKMRRDRLNDRF 94
           L S      P+  E          + E   R R+ + +   +     R +    +L    
Sbjct: 94  LMS------PIKTEQRQPSMMTRMYIEQ--RDRLYNDNQVFAKYNVSRLQPY-LKLRQAL 144

Query: 95  MELASILDPGRPPK------MD---KTVLLADAVQMVTQLRDEAQK---------LKVSN 136
           +EL       RP K      +    KT +  D             +         L + N
Sbjct: 145 LEL-------RPAKNVLIDGVLGSGKTWVALDV------CLSYKVQCKMDFKIFWLNLKN 191

Query: 137 ----EKLLGKINEL----KCEKNELRDEKQRLKNEKENLERQVKALSSQPAFLPHP 184
               E +L  + +L            D    +K    +++ +++ L       P+ 
Sbjct: 192 CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK---PYE 244

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 18/94 (19%), Positives = 38/94 (40%), Gaps = 7/94 (7%)

Query: 86   RRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINE 145
             R RL  +  EL  IL        +    + +  +   QL+ E +K++     L  ++ E
Sbjct: 914  MRVRLAAKKQELEEILH-------EMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEE 966

Query: 146  LKCEKNELRDEKQRLKNEKENLERQVKALSSQPA 179
             +  + +L+ EK     + + +E  +  +  Q  
Sbjct: 967  EEAARQKLQLEKVTADGKIKKMEDDILIMEDQNN 1000

>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 = 14/63 (22%), Positives = 32/63 (50%)

Query: 115  LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
            + D  + + +     QKL++      GKI +++ +   + D+  +L  E++ LE +V  L
Sbjct: 957  MLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDL 1016

Query: 175  SSQ 177
            ++ 
Sbjct: 1017 TTN 1019

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 14/63 (22%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 115  LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL 174
            +A   + + Q + E + ++   +K   +  +L    +EL+++   LK EKE L R++   
Sbjct: 993  IAKLRKELHQTQTEKKTIEEWADKYKHETEQLV---SELKEQNTLLKTEKEELNRRIHDQ 1049

Query: 175  SSQ 177
            + +
Sbjct: 1050 AKE 1052

>2w83_C C-JUN-amino-terminal kinase-interacting protein 4; golgi apparatus, protein transport, ER-golgi transport, ARF, GTPase, effector, myristate; HET: GTP; 1.93A {Homo sapiens} Length = 77

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 18/55 (32%), Positives = 30/55 (54%)

Query: 123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQ 177
           TQL +    L +    L+ K++EL CEK+ L+ E + +K  K  LE + + L  +
Sbjct: 19  TQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKNRELEEE 73

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 387

 Score = 40.8 bits (95), Expect = 2e-04
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 4/59 (6%)

Query: 64  SRKRVRSGSCSASGSKACREKMRRDRLNDRFMELASIL--DPGRPPKMDKTVLLADAVQ 120
           +  + R  +   + S+   EK RRD++N    ELAS++        K+DK  +L  AVQ
Sbjct: 4   AEHQGRIKNAREAHSQI--EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQ 60

>3s9g_A Protein hexim1; cyclin T-binding domain (TBD), cyclin T1/P-TEFB/7SK snRNA, N transcription; 2.10A {Homo sapiens} PDB: 2gd7_A Length = 104

 Score = 37.5 bits (86), Expect = 5e-04
 Identities = 19/73 (26%), Positives = 42/73 (57%), Gaps = 3/73 (4%)

Query: 109 MDKTVLLADAVQM---VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKE 165
           M K  L+ + +++   ++++ DE  +L++ +++L  ++ EL+ E + LR E  +L  E E
Sbjct: 30  MSKQELIKEYLELEKSLSRMEDENNRLRLESKRLDARVRELELELDRLRAENLQLLTENE 89

Query: 166 NLERQVKALSSQP 178
              +Q +A  S+ 
Sbjct: 90  LHRQQERAPLSKF 102

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	99.77
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.75
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.72
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.7
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.68
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.65
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.61
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.57
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.53
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.46
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.44
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.24
4ath_A	83	MITF, microphthalmia-associated transcription fact	99.16
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.14
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.13
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.88
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.71
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	97.91
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	97.7
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	96.94
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	96.61
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	96.44
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	96.38
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	96.15
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	96.13
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	95.82
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	95.32
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	95.29
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	95.28
2oqq_A	42	Transcription factor HY5; homodimer leucine zipper	95.02
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	94.88
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	94.49
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	94.42
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	93.96
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	93.92
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	93.68
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	93.63
3he5_B	52	Synzip2; heterodimeric coiled-coil, de novo protei	93.6
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	93.37
3cve_A	72	Homer protein homolog 1; coiled coil, alternative	93.15
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	92.75
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	92.69
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	92.52
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	92.5
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	92.48
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	92.47
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	92.15
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	92.1
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	91.89
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	91.74
3htk_A	60	Structural maintenance of chromosomes protein 5; S	91.63
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	91.63
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	91.45
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	91.44
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	91.43
3cvf_A	79	Homer-3, homer protein homolog 3; coiled coil, alt	91.38
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	91.36
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	90.91
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	90.75
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	90.65
3he5_A	49	Synzip1; heterodimeric coiled-coil, de novo protei	90.56
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	90.55
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	90.52
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	90.38
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	90.35
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	90.21
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	90.12
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	90.09
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	89.96
1deb_A	54	APC protein, adenomatous polyposis coli protein; c	89.95
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	89.84
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	89.72
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	89.67
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	89.5
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	89.39
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	89.07
3v86_A	27	De novo design helix; computational design of A pr	89.02
2ocy_A	154	RAB guanine nucleotide exchange factor SEC2; RAB,	88.99
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	88.64
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	88.46
3u06_A	412	Protein claret segregational; motor domain, stalk	88.43
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	88.37
2w6a_A	63	ARF GTPase-activating protein GIT1; PIX, zinc, sig	88.27
3swf_A	74	CGMP-gated cation channel alpha-1; coiled-coil, as	88.11
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	88.08
1m1j_C	409	Fibrinogen gamma chain; coiled coils, disulfide ri	88.03
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	88.02
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	87.78
3htk_A	60	Structural maintenance of chromosomes protein 5; S	87.75
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	87.7
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	87.68
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	87.56
2wt7_B	90	Transcription factor MAFB; transcription, transcri	87.48
3swy_A	46	Cyclic nucleotide-gated cation channel alpha-3; co	87.33
2wt7_B	90	Transcription factor MAFB; transcription, transcri	86.86
3iv1_A	78	Tumor susceptibility gene 101 protein; coiled_COIL	86.79
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	86.63
3swk_A	86	Vimentin; cytoskeleton, intermediate filament, alp	86.31
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	86.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	85.68
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	85.68
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	85.67
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	85.42
1kd8_A	36	GABH AIV, GCN4 acid base heterodimer acid-D12IA16V	85.26
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	85.15
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	85.15
3m48_A	33	General control protein GCN4; leucine zipper, synt	85.03
1kd8_B	36	GABH BLL, GCN4 acid base heterodimer base-D12LA16L	84.68
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	84.67
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	84.6
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	84.5
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	84.02
3vmx_A	48	Voltage-gated hydrogen channel 1; coiled-coil, ION	83.66
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	83.39
1wt6_A	81	Myotonin-protein kinase; coiled-coil, kinase activ	83.19
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	83.05
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	83.03
3iv1_A	78	Tumor susceptibility gene 101 protein; coiled_COIL	83.01
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	82.86
2oxj_A	34	Hybrid alpha/beta peptide based on the GCN4-P1 Se	82.8
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	82.75
2j5u_A	255	MREC protein; bacterial cell shape determining pro	82.68
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	82.49
2oxj_A	34	Hybrid alpha/beta peptide based on the GCN4-P1 Se	82.31
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	82.02
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	81.87
1fxk_C	133	Protein (prefoldin); archaeal protein, chaperone;	81.86
3trt_A	77	Vimentin; cytoskeleton, intermediate filament, alp	81.83
3ni0_A	99	Bone marrow stromal antigen 2; coiled-coil, antivi	81.42
2zvf_A	171	Alanyl-tRNA synthetase; C-terminal, oligomerizatio	81.42
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	81.33
3bas_A	89	Myosin heavy chain, striated muscle/general contro	81.29
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	81.13
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	81.12
1uix_A	71	RHO-associated kinase; coiled-coil, transferase; H	80.96
3ibp_A	302	Chromosome partition protein MUKB; structural main	80.68
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	80.52
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	80.19
1wle_A	501	Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bo	80.1
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	80.04
2oto_A	155	M protein; helical coiled coil, fibrinogen-binding	80.03

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

Probab=99.77  E-value=9.3e-19  Score=131.84  Aligned_cols=72  Identities=28%  Similarity=0.423  Sum_probs=65.1

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELK  147 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk  147 (235)
                      ++.+|+.+||+||++||++|.+|+++| |+...|+||++||.+||+||++|+.+++.|+.+++.|+..++..+
T Consensus         6 rr~~H~~~ErrRR~~in~~f~~L~~lv-P~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~~~~~   77 (82)
T 1am9_A            6 KRTAHNAIEKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH-TCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHhc-cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            467899999999999999999999999 555689999999999999999999999999999999988765443

>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=99.75  E-value=1.8e-18  Score=129.62  Aligned_cols=77  Identities=17%  Similarity=0.242  Sum_probs=63.3

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKN  151 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~Ekn  151 (235)
                      ++.+|+.+||+||++||+.|.+|+++||.....|+||++||..||+||++|+.+++.|+.+.+.|..++..|++++.
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~~~~L~~~l~   78 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVR   78 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35689999999999999999999999955445799999999999999999999988887766665555544444443

>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=99.72  E-value=1e-17  Score=128.00  Aligned_cols=78  Identities=26%  Similarity=0.368  Sum_probs=65.8

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGR--PPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNE  152 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~--~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknE  152 (235)
                      .+.+|+.+||+||++||++|..|+++| |..  ..|+||++||.+||+||++|+.+.+.+..+.+.|+.+...|+.++.+
T Consensus         6 ~R~~Hn~~ER~RR~~ln~~f~~Lr~~v-P~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~~~n~~L~~rl~~   84 (88)
T 1nkp_A            6 KRRTHNVLERQRRNELKRSFFALRDQI-PELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQ   84 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTC-GGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999 543  36999999999999999999999998888777666666666555555


Q ss_pred             h
Q 026702          153 L  153 (235)
Q Consensus       153 L  153 (235)
                      |
T Consensus        85 L   85 (88)
T 1nkp_A           85 L   85 (88)
T ss_dssp             H
T ss_pred             h
Confidence            4

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

Probab=99.70  E-value=4.4e-17  Score=122.65  Aligned_cols=77  Identities=21%  Similarity=0.239  Sum_probs=66.4

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHHhhcCCC-CCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 026702           76 SGSKACREKMRRDRLNDRFMELASILDPG-RPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNE  152 (235)
Q Consensus        76 ~~~h~~~ERrRRdklNd~F~~Lr~lLpP~-~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknE  152 (235)
                      +.+|+..||+||+.||++|..|+++||.. ...|++|++||.+||+||++|+.+.++|..+++.|+.+...|+++.+.
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~e~~~L~~~L~~   79 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLEK   79 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            46899999999999999999999999532 347999999999999999999999999998888887777777666554

>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A

Probab=99.68  E-value=3.8e-17  Score=130.80  Aligned_cols=88  Identities=24%  Similarity=0.366  Sum_probs=51.9

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGR--PPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNE  152 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~--~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknE  152 (235)
                      ++.+|+..||+||++||++|.+|+++||++.  ..|+||++||.+||+||++|+.+++.|+++...           ...
T Consensus        27 kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~~-----------~~~   95 (118)
T 4ati_A           27 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENR-----------QKK   95 (118)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC---------------
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHH
Confidence            5889999999999999999999999995543  248999999999999999999999998875322           123


Q ss_pred             hHHHHHHHHHHHHHHHHHHHH
Q 026702          153 LRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       153 Lr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      |+.++..|...+..||.|.++
T Consensus        96 l~~~n~~L~~riqeLE~~a~~  116 (118)
T 4ati_A           96 LEHANRHLLLRVQELEMQARA  116 (118)
T ss_dssp             ---------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            455555565566666655543

>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=99.65  E-value=1.5e-16  Score=118.70  Aligned_cols=68  Identities=18%  Similarity=0.288  Sum_probs=60.8

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK  142 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~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            57889999999999999999999999954444699999999999999999999999998888877643

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.61  E-value=5.2e-16  Score=115.03  Aligned_cols=58  Identities=33%  Similarity=0.492  Sum_probs=52.5

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLK  133 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk  133 (235)
                      .+.+|+..||+||++||++|.+|+++| |+...|+||++||..||+||++|+.++.=|+
T Consensus         8 kR~~Hn~iErrRRd~IN~~i~eL~~Lv-P~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            8 KRVSRNKSEKKRRDQFNVLIKELGSML-PGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTS-SSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HhhhhhHHHhhHHHHHHHHHHHHHHhC-CCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            477899999999999999999999999 5556799999999999999999999876554

>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=99.57  E-value=9.5e-16  Score=110.05  Aligned_cols=56  Identities=21%  Similarity=0.359  Sum_probs=49.5

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCC----CCCchhhhHHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGRP----PKMDKTVLLADAVQMVTQLRDEAQ  130 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~----~K~dKasIL~dAI~yIk~Lr~~vq  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            57899999999999999999999999955432    389999999999999999997653

>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=99.53  E-value=2.6e-15  Score=108.35  Aligned_cols=55  Identities=24%  Similarity=0.324  Sum_probs=48.4

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCC-----CCCCCchhhhHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPG-----RPPKMDKTVLLADAVQMVTQLRDEA  129 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~-----~~~K~dKasIL~dAI~yIk~Lr~~v  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            478999999999999999999999999532     1368899999999999999998765

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.46  E-value=1e-14  Score=108.26  Aligned_cols=54  Identities=37%  Similarity=0.419  Sum_probs=47.5

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCC--CCCCCchhhhHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPG--RPPKMDKTVLLADAVQMVTQLRDE  128 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~--~~~K~dKasIL~dAI~yIk~Lr~~  128 (235)
                      ++.+|+..||+||++||++|.+|+++||.+  ...|+||++||..||+||+.|+..
T Consensus         9 rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~~   64 (73)
T 4h10_A            9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   64 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhcC
Confidence            577899999999999999999999999432  136999999999999999999753

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A*

Probab=99.44  E-value=3.9e-14  Score=105.85  Aligned_cols=60  Identities=23%  Similarity=0.378  Sum_probs=48.5

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHHhhcCCC-CCCCC-chhhhHHHHHHHHHHHHHHHHHHH
Q 026702           74 SASGSKACREKMRRDRLNDRFMELASILDPG-RPPKM-DKTVLLADAVQMVTQLRDEAQKLK  133 (235)
Q Consensus        74 ~~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~-~~~K~-dKasIL~dAI~yIk~Lr~~vq~Lk  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            4678999999999999999999999999532 23465 899999999999999999998764

>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=99.24  E-value=2.2e-12  Score=94.58  Aligned_cols=56  Identities=18%  Similarity=0.303  Sum_probs=49.8

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHH
Q 026702           74 SASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEA  129 (235)
Q Consensus        74 ~~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~v  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            46788999999999999999999999995433469999999999999999998754

>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus}

Probab=99.16  E-value=3.2e-10  Score=86.33  Aligned_cols=76  Identities=25%  Similarity=0.377  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHhhcCCC--CCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHH
Q 026702           87 RDRLNDRFMELASILDPG--RPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEK  164 (235)
Q Consensus        87 RdklNd~F~~Lr~lLpP~--~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~  164 (235)
                      |..||++|.+|+.+||+.  ...|.+|++||..||+||+.|++++++++++...+           ..|...+..|.-.+
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r~-----------k~le~~n~~l~~ri   72 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQ-----------KKLEHANRHLLLRV   72 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHHH-----------HHHHHHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHhhhhhHHHHHHH
Confidence            889999999999999653  23699999999999999999999998888754432           12333444444445


Q ss_pred             HHHHHHHHH
Q 026702          165 ENLERQVKA  173 (235)
Q Consensus       165 e~Le~qlk~  173 (235)
                      -.||-|.++
T Consensus        73 qELE~qa~~   81 (83)
T 4ath_A           73 QELEMQARA   81 (83)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            455555443

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.14  E-value=3.7e-11  Score=108.54  Aligned_cols=53  Identities=34%  Similarity=0.541  Sum_probs=42.6

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDE  128 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~  128 (235)
                      ++.+|+..||+||++||+.|.+|+++| |+...|+||++||..||.||+.|+..
T Consensus        12 ~~~~~~~~e~~rr~~~n~~~~~l~~~~-p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           12 KRVSRNKSEKKRRDQFNVLIKELGSML-PGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHTC-CSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHhC-CCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            477899999999999999999999999 55567999999999999999998754

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}

Probab=99.13  E-value=4.3e-11  Score=85.59  Aligned_cols=56  Identities=20%  Similarity=0.162  Sum_probs=48.3

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCC-CCCCCchhhhHHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPG-RPPKMDKTVLLADAVQMVTQLRDEAQ  130 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~-~~~K~dKasIL~dAI~yIk~Lr~~vq  130 (235)
                      ++..|+.+||+|+..||+.|..|+.+||.. ...|.+|+.||..||+||..|++.++
T Consensus         2 rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            356789999999999999999999999432 24699999999999999999997653

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=98.88  E-value=6.9e-10  Score=101.58  Aligned_cols=54  Identities=37%  Similarity=0.419  Sum_probs=47.6

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCC--CCCCCchhhhHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPG--RPPKMDKTVLLADAVQMVTQLRDE  128 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~--~~~K~dKasIL~dAI~yIk~Lr~~  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            478899999999999999999999999421  247999999999999999999853

>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=98.71  E-value=3.9e-09  Score=77.69  Aligned_cols=49  Identities=14%  Similarity=0.206  Sum_probs=42.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhcCCC-CCCCCchhhhHHHHHHHHHHHHH
Q 026702           79 KACREKMRRDRLNDRFMELASILDPG-RPPKMDKTVLLADAVQMVTQLRD  127 (235)
Q Consensus        79 h~~~ERrRRdklNd~F~~Lr~lLpP~-~~~K~dKasIL~dAI~yIk~Lr~  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            34699999999999999999999421 23599999999999999999974

>4aya_A DNA-binding protein inhibitor ID-2; cell cycle; 2.10A {Homo sapiens}

Probab=97.91  E-value=1.7e-05  Score=61.79  Aligned_cols=51  Identities=14%  Similarity=0.165  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCC-CCCCCchhhhHHHHHHHHHHHHHHHHH
Q 026702           81 CREKMRRDRLNDRFMELASILDPG-RPPKMDKTVLLADAVQMVTQLRDEAQK  131 (235)
Q Consensus        81 ~~ERrRRdklNd~F~~Lr~lLpP~-~~~K~dKasIL~dAI~yIk~Lr~~vq~  131 (235)
                      ..||.|=..||+.|..||..||.. ...|.+|..||.-||+||..|+..++.
T Consensus        31 ~~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~   82 (97)
T 4aya_A           31 DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS   82 (97)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhc
Confidence            345778888999999999999421 236999999999999999999987654

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=97.70  E-value=0.0003  Score=53.26  Aligned_cols=60  Identities=25%  Similarity=0.448  Sum_probs=52.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      +..||+-|.-|+-++..|+.+|..|.++..+++.....|+.|+.+|+.|...++..|.++
T Consensus        15 Iq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~~L   74 (81)
T 2jee_A           15 VQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQAL   74 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            357889999999999999999999999999999999999999999999988888777653

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=96.94  E-value=0.0054  Score=46.35  Aligned_cols=56  Identities=27%  Similarity=0.325  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHH-------HHHHHHHHHHHHHHh
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQR-------LKNEKENLERQVKAL  174 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            36788999999999999999999999999888888888877       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=96.61  E-value=0.012  Score=41.78  Aligned_cols=58  Identities=22%  Similarity=0.230  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHH
Q 026702           83 EKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRD  155 (235)
Q Consensus        83 ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~  155 (235)
                      ||++|-+..++..+-+.--               .-..|+.+|+.++..|+.+|..|..+|..|+.|+..|+.
T Consensus         1 Ekr~rrrerNR~AA~rcR~---------------rKk~~~~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk~   58 (63)
T 2wt7_A            1 EKRRIRRERNKMAAAKCRN---------------RRRELTDTLQAETDQLEDEKSALQTEIANLLKEKEKLEF   58 (63)
T ss_dssp             CHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHhHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566666666777766654               224788888888888888888887777666666555443

>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=96.44  E-value=0.0044  Score=45.45  Aligned_cols=42  Identities=17%  Similarity=0.174  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRL  160 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~L  160 (235)
                      -.||++|+.+|..|+..+..|..++..|+.++..|+.|+..|
T Consensus        28 ~~~i~~LE~~v~~le~~~~~l~~en~~Lr~~i~~L~~El~~l   69 (70)
T 1gd2_E           28 EDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRIL   69 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            468888888888888877776666655555555555555443

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=96.38  E-value=0.031  Score=45.47  Aligned_cols=83  Identities=16%  Similarity=0.115  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHhh--cCCCCCCCCchhhhHHH---HHHHH------HHHHHHHH-------HHHHHHHHHHHHHHHHHHH
Q 026702           88 DRLNDRFMELASI--LDPGRPPKMDKTVLLAD---AVQMV------TQLRDEAQ-------KLKVSNEKLLGKINELKCE  149 (235)
Q Consensus        88 dklNd~F~~Lr~l--LpP~~~~K~dKasIL~d---AI~yI------k~Lr~~vq-------~Lk~~n~~L~~ei~~Lk~E  149 (235)
                      ..+|+++.+++..  - |.  --.++.+||.-   |=+|+      ..|+.+++       .|+.++..++.+++.++.+
T Consensus        35 ~~vd~km~ei~~~~~~-~~--l~~~r~aVLaALNiadEl~k~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e  111 (138)
T 3hnw_A           35 SYINNKITEFNKEESY-RR--MSAELRTDMMYLNIADDYFKAKKMADSLSLDIENKDKEIYDLKHELIAAQIKAESSAKE  111 (138)
T ss_dssp             HHHHHHHHHHTTCHHH-HT--SCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCC-CC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999966  6 42  36688888763   11222      22222333       3333344444445555555


Q ss_pred             HhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          150 KNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       150 knELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +.+|++++..|+.++-+||..++.
T Consensus       112 ~~~l~~~~~~l~~~~~~le~~~~~  135 (138)
T 3hnw_A          112 IKELKSEINKYQKNIVKLETELND  135 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            566666666666666666655543

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=96.15  E-value=0.023  Score=46.27  Aligned_cols=45  Identities=24%  Similarity=0.322  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKE  165 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e  165 (235)
                      -|..|+.++..++..++.+..++.+|+.++++|+.++..|.++.+
T Consensus        90 E~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~~  134 (138)
T 3hnw_A           90 EIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETELN  134 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334455555555555555555555555555555555555555443

>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=96.13  E-value=0.026  Score=44.18  Aligned_cols=58  Identities=26%  Similarity=0.382  Sum_probs=36.1

Q ss_pred             CCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          108 KMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGK-------INELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       108 K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~e-------i~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      .|+|..++.+-+    +|...+..|+.++..|+..       |.+|..|+..|+.||+.|+.|.+-..+
T Consensus        29 ~mSKqELIqEYl----~LE~~~s~le~e~~rlr~~~~~~~~~v~eLe~everL~~ENq~L~~e~~~~~~   93 (104)
T 3s9g_A           29 NMSKQELIKEYL----ELEKSLSRMEDENNRLRLESKRLDARVRELELELDRLRAENLQLLTENELHRQ   93 (104)
T ss_dssp             TSCHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHHHH----HHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            678888887543    3777777788877777764       455555555555555555554444433

>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=95.82  E-value=0.013  Score=40.74  Aligned_cols=39  Identities=15%  Similarity=0.256  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHhHhHH
Q 026702          117 DAVQMVTQLRD-------EAQKLKVSNEKLLGKINELKCEKNELRD  155 (235)
Q Consensus       117 dAI~yIk~Lr~-------~vq~Lk~~n~~L~~ei~~Lk~EknELr~  155 (235)
                      +|++||++--+       .++.|+.+|+.|+.++..|+.+..||+.
T Consensus         2 ~AlefIk~~LG~~~p~~~d~eaLk~E~~eLk~k~~~L~~~~~el~~   47 (53)
T 2yy0_A            2 SALDFLKHHLGAATPENPEIELLRLELAEMKEKYEAIVEENKKLKA   47 (53)
T ss_dssp             --------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68889887643       3455555555555444444444444433

>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=95.32  E-value=0.038  Score=38.65  Aligned_cols=34  Identities=26%  Similarity=0.338  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHh
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNEL  153 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknEL  153 (235)
                      .|+.+|+.++..|+.+|..|..++..|+.|+..|
T Consensus        22 ~~~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~L   55 (61)
T 1t2k_D           22 VWVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQL   55 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555566666666555555555544444444333

>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=95.29  E-value=0.066  Score=41.79  Aligned_cols=55  Identities=22%  Similarity=0.333  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh----------------------------HhHHHHHHHHHHHHHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKN----------------------------ELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~Ekn----------------------------ELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      -+..|+.+++.|+.+++.|.++++.|+.++.                            ..+.+...|++|+++|...++
T Consensus        13 ~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~~l~Gd~~~~~TKVlH~~~NPa~~a~~~~~~~~e~Lq~E~erLr~~v~   92 (100)
T 1go4_E           13 EADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAECERLRGLLR   92 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCSCCCTTTEEEEEESSCHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCccCeeeeecCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556677777777777777776666655553                            234445567777777776666


Q ss_pred             Hhc
Q 026702          173 ALS  175 (235)
Q Consensus       173 ~~~  175 (235)
                      .|.
T Consensus        93 ~lE   95 (100)
T 1go4_E           93 AME   95 (100)
T ss_dssp             TCC
T ss_pred             HHh
Confidence            543

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=95.28  E-value=0.13  Score=42.94  Aligned_cols=85  Identities=13%  Similarity=0.049  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Q 026702           87 RDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKEN  166 (235)
Q Consensus        87 RdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~  166 (235)
                      |+.+-.+|.+|-.-+ .+.++. +=+|=+..-+.-|..|+.+...|+..+..|.+++++-......|+||...|..+..-
T Consensus        37 Rd~~E~~~~~l~~e~-~~~~~~-~~vs~~~~~~~~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~  114 (152)
T 3a7p_A           37 RNDKEAHLNELFQDN-SGAIGG-NIVSHDDALLNTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNV  114 (152)
T ss_dssp             ---------------------C-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHhh-ccCCCc-ccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            666655666665554 211111 122333344567777777777777777777777766666667788888877777777


Q ss_pred             HHHHHHH
Q 026702          167 LERQVKA  173 (235)
Q Consensus       167 Le~qlk~  173 (235)
                      ++..++.
T Consensus       115 lE~kl~k  121 (152)
T 3a7p_A          115 LQQKLSD  121 (152)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7776654

>2oqq_A Transcription factor HY5; homodimer leucine zipper; 2.00A {Arabidopsis thaliana}

Probab=95.02  E-value=0.059  Score=36.04  Aligned_cols=36  Identities=22%  Similarity=0.414  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRD  155 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~  155 (235)
                      .|+.+|+.++..|+..|..|.+.+..|..|...||.
T Consensus         3 aYl~eLE~r~k~le~~naeLEervstLq~EN~mLRq   38 (42)
T 2oqq_A            3 AYLSELENRVKDLENKNSELEERLSTLQNENQMLRH   38 (42)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            599999999999999999999988888877777664

>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=94.88  E-value=0.042  Score=38.64  Aligned_cols=35  Identities=23%  Similarity=0.420  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELR  154 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr  154 (235)
                      +|+.+|+.++..|+.+|..|..++..|+.|+..|+
T Consensus        22 ~~~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~~Lk   56 (62)
T 1jnm_A           22 ERIARLEEKVKTLKAQNSELASTANMLREQVAQLK   56 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56667777777777776666666655555554443

>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=94.49  E-value=0.11  Score=38.39  Aligned_cols=48  Identities=21%  Similarity=0.153  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le  168 (235)
                      -|.+|+..+++-.+++...++.|++|..++.|..++...|+.++++++
T Consensus        20 ti~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKfr   67 (72)
T 3nmd_A           20 SLRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDKYR   67 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            388888888888888888888899999999999998898888888774

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=94.42  E-value=0.38  Score=36.53  Aligned_cols=54  Identities=24%  Similarity=0.396  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLL------------GKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~------------~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +-|+.|+.+...|+.+...++            .+|.+|+.++.++..|+.+|..|++.|+..+..
T Consensus        23 dKVR~LEqqN~~Le~~i~~l~~~~~~~~~~~ye~~i~~Lr~~i~~~~~ek~~l~~e~dnl~~~~~~   88 (93)
T 3s4r_A           23 DKVRFLEQQNKILLAELEQLKGQGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAEDIMR   88 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445556666666665544433            457778888888888888888888887776654

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1

Probab=93.96  E-value=0.16  Score=35.47  Aligned_cols=37  Identities=24%  Similarity=0.293  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          135 SNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       135 ~n~~L~~ei~~Lk~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            3455666666666666667777777777776666654

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=93.92  E-value=0.26  Score=46.20  Aligned_cols=39  Identities=18%  Similarity=0.237  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH----hcCCCC
Q 026702          141 GKINELKCEKNELRDEKQRLKNEKENLERQVKA----LSSQPA  179 (235)
Q Consensus       141 ~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~----~~~~p~  179 (235)
                      .++.+++....+.++....|+.|...+.++++.    .+.+|+
T Consensus       544 ~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~~~~~~~  586 (597)
T 3oja_B          544 QENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAKKNRNPD  586 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC----
T ss_pred             hhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            333334443334444445555555555555554    345554

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=93.68  E-value=0.47  Score=35.94  Aligned_cols=53  Identities=21%  Similarity=0.232  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      |...-+.....-+.+-++-.....++..+..+|..||..|+.+++.|+.++..
T Consensus        16 Y~~rR~rNN~AarrSR~krk~r~~e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~   68 (87)
T 1hjb_A           16 YKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELST   68 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44443333333444444434444445555555666666666666666555544

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=93.63  E-value=0.072  Score=36.96  Aligned_cols=31  Identities=23%  Similarity=0.309  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEK  150 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~Ek  150 (235)
                      .||.+|+.+|..|+.+|..|..++..|+.+.
T Consensus        22 ~~~~~LE~~v~~L~~eN~~L~~~~~~L~~~~   52 (55)
T 1dh3_A           22 EYVKSLENRVAVLENQNKTLIEELKALKDLY   52 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6777777777777777777776666665543

>3he5_B Synzip2; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=93.60  E-value=0.2  Score=34.04  Aligned_cols=43  Identities=35%  Similarity=0.373  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKEN  166 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~  166 (235)
                      .|++.+..|++.|-+|+..-..|..-+..||+|..+|..|...
T Consensus         7 ylrkkiarlkkdnlqlerdeqnlekiianlrdeiarlenevas   49 (52)
T 3he5_B            7 YLRKKIARLKKDNLQLERDEQNLEKIIANLRDEIARLENEVAS   49 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHHHHHHHHHhh
Confidence            4888999999999888877777777778888887777666543

>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=93.37  E-value=0.6  Score=34.63  Aligned_cols=55  Identities=22%  Similarity=0.258  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            5555544444555555555555555666666777777777777777777776654

>3cve_A Homer protein homolog 1; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, postsynaptic cell membrane, synapse; 1.75A {Rattus norvegicus}

Probab=93.15  E-value=0.4  Score=35.29  Aligned_cols=51  Identities=14%  Similarity=0.287  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +.+..+++.++..|..|++.+..|+...++-+.+-..++.|+.++-++|..
T Consensus         3 ~~~~~kLq~~E~~N~~Le~~v~~le~~Le~s~~~q~~~~~Elk~~~e~Ld~   53 (72)
T 3cve_A            3 HNSHMKLQEVEIRNKDLEGQLSEMEQRLEKSQSEQDAFRSNLKTLLEILDG   53 (72)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            356677888888888888888888888888888888888888887776543

>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D

Probab=92.75  E-value=0.36  Score=33.97  Aligned_cols=37  Identities=32%  Similarity=0.409  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          136 NEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       136 n~~L~~ei~~Lk~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            4556666666666666666666666666666666654

>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus norvegicus}

Probab=92.69  E-value=0.54  Score=35.87  Aligned_cols=48  Identities=19%  Similarity=0.461  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      +..|+.+++.|+.+-..|..++..|..+...|..+...++.+.++|.+
T Consensus         6 ~~~l~~eL~~l~~eE~~L~~eL~~lEke~~~l~~el~~le~E~~~L~~   53 (96)
T 3q8t_A            6 SEQLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQ   53 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhh
Confidence            355666666666666666666666666666666666666666666655

>2dgc_A Protein (GCN4); basic domain, leucine zipper, DNA binding, eukaryotic regulatory protein, transcription/DNA complex; HET: DNA; 2.20A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 1dgc_A* 1ld4_E 1ysa_C* 3p8m_D

Probab=92.52  E-value=0.17  Score=35.94  Aligned_cols=29  Identities=28%  Similarity=0.405  Sum_probs=13.3

Q ss_pred             HHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          143 INELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       143 i~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      +.+|..+..+|..+|..|+.+++.|.++|
T Consensus        32 ~~~Le~~v~~L~~eN~~L~~ev~~Lr~~l   60 (63)
T 2dgc_A           32 MKQLEDKVEELLSKNYHLENEVARLKKLV   60 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444555555554444

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=92.50  E-value=0.68  Score=36.61  Aligned_cols=22  Identities=32%  Similarity=0.394  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKI  143 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei  143 (235)
                      +++|+..+..|+.+++.++.+.
T Consensus         5 ~rdL~~~~~~L~~E~e~~k~K~   26 (111)
T 2v66_B            5 NRDLQADNQRLKYEVEALKEKL   26 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555555555554443

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1

Probab=92.48  E-value=0.75  Score=32.43  Aligned_cols=42  Identities=26%  Similarity=0.222  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRL  160 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~L  160 (235)
                      .+|=..=+.+.+.|+.+.+.|..+..+|+.+++.|+.|+..|
T Consensus        15 ~R~R~KKk~~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~L   56 (63)
T 1ci6_A           15 TRYRQKKRAEQEALTGECKELEKKNEALKERADSLAKEIQYL   56 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334333333444444444444444444444444444444333

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=92.47  E-value=1.6  Score=34.57  Aligned_cols=15  Identities=33%  Similarity=0.536  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHHHHH
Q 026702          159 RLKNEKENLERQVKA  173 (235)
Q Consensus       159 ~Lk~e~e~Le~qlk~  173 (235)
                      ++..+|+.|+.||..
T Consensus        87 kl~~eKe~L~~ql~~  101 (110)
T 2v4h_A           87 KLVEKKEYLQEQLEQ  101 (110)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHH
Confidence            455555555555544

>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=92.15  E-value=2.7  Score=39.34  Aligned_cols=45  Identities=20%  Similarity=0.320  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          129 AQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       129 vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .++++++.+.++..+++.+....|+++|++.+++|+..|++.+..
T Consensus       539 ~~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~~~~  583 (597)
T 3oja_B          539 TEDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAKKNR  583 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             hhhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            344445566677777777777777777777777777777777665

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A

Probab=92.10  E-value=0.15  Score=35.69  Aligned_cols=36  Identities=25%  Similarity=0.411  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          136 NEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       136 n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      ...|+.++..|..+..+|+.+...|+.|+..|.++|
T Consensus        24 ~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~~Lk~~l   59 (62)
T 1jnm_A           24 IARLEEKVKTLKAQNSELASTANMLREQVAQLKQKV   59 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444555555555555555555555555554444

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=91.89  E-value=1.8  Score=34.39  Aligned_cols=67  Identities=21%  Similarity=0.350  Sum_probs=33.7

Q ss_pred             CCchhhhHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          108 KMDKTVLLADAVQMVTQLRDEAQKLKVSN----EKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       108 K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n----~~L~~ei~~Lk~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            34444333333333444444444443322    23444455555565555555566666677777766653

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=91.74  E-value=1.2  Score=33.48  Aligned_cols=55  Identities=20%  Similarity=0.250  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          118 AVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       118 AI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      =|.-|++|+-.|..|+.+..+-.-+++.-|.|+..|++....=.+++++|+.||-
T Consensus        24 L~qEi~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l~   78 (81)
T 3qh9_A           24 LLQELRHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQLS   78 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHHh
Confidence            3467888888888887665555555666777777788877777788888888774

>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=91.63  E-value=1.7  Score=29.60  Aligned_cols=53  Identities=13%  Similarity=0.120  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      -+..|+..+..++.....+..+...++...+++..+....+.++.+++.|++.
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi~~   58 (60)
T 3htk_A            6 TKKTLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEY   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34555555555555555555666666666666666666666677777666653

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=91.63  E-value=0.24  Score=44.25  Aligned_cols=19  Identities=21%  Similarity=0.401  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHHhcCCCC
Q 026702          161 KNEKENLERQVKALSSQPA  179 (235)
Q Consensus       161 k~e~e~Le~qlk~~~~~p~  179 (235)
                      +.|+++|+.||+.+..||.
T Consensus        81 r~El~~LkeElerL~sPPL   99 (251)
T 3m9b_A           81 RQQLLALREEVDRLGQPPS   99 (251)
T ss_dssp             HHHHHHHHHHHHHHHSCCE
T ss_pred             HHHHHHHHHHHHHhcCCCc
Confidence            3344444455555566663

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=91.45  E-value=0.51  Score=43.97  Aligned_cols=54  Identities=19%  Similarity=0.276  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      |.+|+.++..|+++...|+++++.++.+..+|.+..........+|..+++.+.
T Consensus         5 ~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~rr~l~n~~~elk   58 (403)
T 4etp_A            5 IAALKEKIAALKEKIAALKEKIKDTELGMKELNEILIKEETVRRTLHNELQELR   58 (403)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            456788888888888888888888888888888877777777777777777753

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=91.44  E-value=0.21  Score=44.61  Aligned_cols=41  Identities=20%  Similarity=0.271  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          129 AQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       129 vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      +.+|+.++..|..+.++|+.+.+++++|...||.|+++|.+
T Consensus        56 l~eL~~ql~~L~arNe~L~~~Lk~ar~El~~LkeElerL~s   96 (251)
T 3m9b_A           56 IHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRLGQ   96 (251)
T ss_dssp             HHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            33444555555555555666677777777778888888766

>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=91.43  E-value=0.4  Score=34.96  Aligned_cols=38  Identities=18%  Similarity=0.230  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          136 NEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       136 n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +..|+.++.+|..+...|..|+..|+.+++.|..+++.
T Consensus        31 i~~LE~~v~~le~~~~~l~~en~~Lr~~i~~L~~El~~   68 (70)
T 1gd2_E           31 LKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRI   68 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555566666667777777777777777654

>3cvf_A Homer-3, homer protein homolog 3; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, phosphoprotein, polymorphism; 2.90A {Homo sapiens}

Probab=91.38  E-value=0.66  Score=34.67  Aligned_cols=49  Identities=18%  Similarity=0.301  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      +..+++.++..|..|++.+..|+...++-+.+-..++.|+.++-++|..
T Consensus        11 ~~~klq~~E~rN~~Le~~v~~le~~Le~s~~~q~~~~~Elk~l~e~Ld~   59 (79)
T 3cvf_A           11 TQQKVQDLETRNAELEHQLRAMERSLEEARAERERARAEVGRAAQLLDV   59 (79)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4456777777888888888888888888888878888888877776543

>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=37.80  Aligned_cols=52  Identities=27%  Similarity=0.323  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HhHhHHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCE----KNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~E----knELr~E~~~Lk~e~e~Le~ql  171 (235)
                      .-+++|+.++..|+.+++.++.+.+....+    .+.|++|.+.|+..++.|...|
T Consensus        56 k~~~~L~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~el~~l~~~~~~l~~~i  111 (189)
T 2v71_A           56 QRNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYV  111 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444443333333333    4444555445554444444443

>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=90.91  E-value=1.2  Score=38.36  Aligned_cols=38  Identities=21%  Similarity=0.357  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNE  152 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknE  152 (235)
                      +.=++.-+..|+.++..|..+|+.|+.+++.|..+..+
T Consensus       127 fd~~~~~~~~~~~~~~~L~~e~~~l~~~~~~l~~qlE~  164 (213)
T 1ik9_A          127 IAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEK  164 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55555555555555555555555554444444444433

>3m91_A Proteasome-associated ATPase; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis} PDB: 3m9h_A

Probab=90.75  E-value=0.78  Score=31.62  Aligned_cols=41  Identities=27%  Similarity=0.416  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      +-+.+|+.++..|...|++|.+..+       +-|++...|+.++++|
T Consensus         9 ~r~~~l~~~l~~L~~rN~rL~~~L~-------~AR~el~~Lkeele~L   49 (51)
T 3m91_A            9 RDIHQLEARIDSLAARNSKLMETLK-------EARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHh
Confidence            3455677777777777777755544       4444555555566655

>2fxo_A Myosin heavy chain, cardiac muscle beta isoform; coiled coil (dimeric, parallel), familial hypertrophic cardiomyopathy, FHC-associated mutant E924K; 2.50A {Homo sapiens} SCOP: h.1.26.1 PDB: 2fxm_A

Probab=90.65  E-value=2.1  Score=33.73  Aligned_cols=62  Identities=24%  Similarity=0.329  Sum_probs=42.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          113 VLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       113 sIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      ..+.+|-+....|...-..|+..+..|.+.+.+.....++|..++..|..+++.|+.+|...
T Consensus        62 ~~l~e~EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~Lk~~led~  123 (129)
T 2fxo_A           62 DNLADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSELKRDIDDL  123 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667777777777777777777766666666666666666666777777777777666653

>3he5_A Synzip1; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=90.56  E-value=1.1  Score=30.06  Aligned_cols=23  Identities=39%  Similarity=0.510  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGK  142 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~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            45788999999999999988754

>1go4_E MAD1 (mitotic arrest deficient)-like 1; mitotic spindle checkpoint, cell cycle, mitosis, nuclear Pro; 2.05A {Homo sapiens} SCOP: h.1.22.1

Probab=90.55  E-value=0.57  Score=36.48  Aligned_cols=42  Identities=29%  Similarity=0.385  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 026702          141 GKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAFLP  182 (235)
Q Consensus       141 ~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~~~p~~~p  182 (235)
                      +++..|+.++++|+.|+.+|+.+++.||-+|......-.|-|
T Consensus        12 e~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~~l~Gd~~~   53 (100)
T 1go4_E           12 EEADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQGDYDQ   53 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCSCCCT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCC
Confidence            456778888888888888888899999999888554334433

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=90.52  E-value=0.69  Score=48.23  Aligned_cols=17  Identities=47%  Similarity=0.730  Sum_probs=8.1

Q ss_pred             HhHHHHHHHHHHHHHHH
Q 026702          152 ELRDEKQRLKNEKENLE  168 (235)
Q Consensus       152 ELr~E~~~Lk~e~e~Le  168 (235)
                      .|++|++.|+++++.|+
T Consensus      1027 ~L~~e~~~L~qq~~~l~ 1043 (1080)
T 2dfs_A         1027 ELKEQNTLLKTEKEELN 1043 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            34444444444444444

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=90.38  E-value=1.1  Score=35.61  Aligned_cols=51  Identities=18%  Similarity=0.273  Sum_probs=35.7

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          112 TVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       112 asIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      -.|..++=+||.+|+.+|..|+.+++.-+.       ++.+...|+..|+.+++.|+.
T Consensus        32 e~l~~E~q~~v~ql~~~i~~Le~eL~e~r~-------~~q~a~~e~e~Lr~e~~~l~~   82 (120)
T 3i00_A           32 ENMKTESQRVVLQLKGHVSELEADLAEQQH-------LRQQAADDCEFLRAELDELRR   82 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH
Confidence            357889999999999999999988766443       344555555566666665533

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=90.35  E-value=1  Score=46.99  Aligned_cols=23  Identities=17%  Similarity=0.215  Sum_probs=14.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhc
Q 026702          153 LRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       153 Lr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      |++....|+.|+.+|++|+..++
T Consensus      1021 L~~kv~~L~~e~~~L~qq~~~l~ 1043 (1080)
T 2dfs_A         1021 TEQLVSELKEQNTLLKTEKEELN 1043 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444567777777777766543

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=90.21  E-value=1.3  Score=33.61  Aligned_cols=32  Identities=19%  Similarity=0.353  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          137 EKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       137 ~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le  168 (235)
                      ..|+..+..+..++..|.-|...|..+.++++
T Consensus        59 ~~Lr~~i~~~~~ek~~l~~e~dnl~~~~~~~k   90 (93)
T 3s4r_A           59 RELRRQVDQLTNDKARVEVERDNLAEDIMRLR   90 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444443

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=90.12  E-value=2  Score=36.15  Aligned_cols=75  Identities=21%  Similarity=0.389  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Q 026702           87 RDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKEN  166 (235)
Q Consensus        87 RdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~  166 (235)
                      |+.|-.-+..|.+.|.-   .+.+    ...+-+.|.+|+.+++.|..+++.+......+..++..|.+....|..++..
T Consensus        64 k~~Leke~~~LQa~L~q---Er~~----r~q~se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r~L~Ekl~~lEKe~a~  136 (168)
T 3o0z_A           64 KSQTDKDYYQLQAILEA---ERRD----RGHDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEAQDMLNHSEKEKNN  136 (168)
T ss_dssp             HHHHHHHHHHHHHHHHH---HHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH---HHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44455555555555522   1111    2233455556666666666666555555555555555555555555555555


Q ss_pred             HH
Q 026702          167 LE  168 (235)
Q Consensus       167 Le  168 (235)
                      ++
T Consensus       137 ~e  138 (168)
T 3o0z_A          137 LE  138 (168)
T ss_dssp             HH
T ss_pred             hh
Confidence            55

>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=90.09  E-value=0.75  Score=36.91  Aligned_cols=34  Identities=29%  Similarity=0.410  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          136 NEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       136 n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      .+.|+.||+.|+.++.+...|..+|+.+.+-|..
T Consensus        73 vqeLqgEI~~Lnq~Lq~a~ae~erlr~~~~~~~~  106 (121)
T 3mq7_A           73 VEELEGEITTLNHKLQDASAEVERLRRENQVLSV  106 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhchhhhh
Confidence            3444444444444444444444444444443333

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=89.96  E-value=1.5  Score=34.02  Aligned_cols=52  Identities=17%  Similarity=0.206  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          117 DAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       117 dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le  168 (235)
                      ++-+-|.+|+.++...+.+...|..+..+-+....+...++..+..|+|.|-
T Consensus         9 ~lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLT   60 (97)
T 2eqb_B            9 QLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLT   60 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444443333333333333333444444444433

>1deb_A APC protein, adenomatous polyposis coli protein; coiled coil, tumor suppressor, structural protein; 2.40A {Homo sapiens} SCOP: h.1.18.1

Probab=89.95  E-value=1.6  Score=30.29  Aligned_cols=45  Identities=22%  Similarity=0.316  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702          123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      .||-.+|+.|+.+|..|+.|.++=...++.|..|...+|.=...|
T Consensus         6 dQL~~QVe~Lk~ENshLrrEL~dNS~~lskLE~ets~mKevlk~l   50 (54)
T 1deb_A            6 DQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQL   50 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHhhHHHHHHHHhhhhhHHHHHHHH
Confidence            467888999999999888877766666666666666665444443

>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=89.84  E-value=1.3  Score=43.44  Aligned_cols=75  Identities=16%  Similarity=0.146  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHH
Q 026702           87 RDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVT-QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKE  165 (235)
Q Consensus        87 RdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk-~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e  165 (235)
                      |..++..+..+..+|   + .+...+.=+..++.-|. +|+.+++-|+.++..-...|+.|+.-+.+++.+.++|..+|+
T Consensus        80 sKdseqy~k~~~E~L---r-~rq~q~~dNdNtynE~S~ELRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvDId  155 (562)
T 3ghg_A           80 NKDSHSLTTNIMEIL---R-GDFSSANNRDNTYNRVSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDID  155 (562)
T ss_dssp             HHHHHHHHHHHHHTT---S-SHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHH---H-HHHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566677777777   2 23344444455554444 888888888887765557788888888888888888877764

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=89.72  E-value=0.59  Score=35.38  Aligned_cols=29  Identities=24%  Similarity=0.370  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNE  152 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknE  152 (235)
                      +++.++..|+.+|..|+.+|..|+.|...
T Consensus        40 e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~   68 (87)
T 1hjb_A           40 ETQHKVLELTAENERLQKKVEQLSRELST   68 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555555444444443

>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=89.67  E-value=1.4  Score=30.39  Aligned_cols=37  Identities=19%  Similarity=0.334  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          138 KLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       138 ~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      .|+.++..|......|-+-....+.++++|..+|..+
T Consensus        13 ~l~~~l~~L~~rN~rL~~~L~~AR~el~~Lkeele~L   49 (51)
T 3m91_A           13 QLEARIDSLAARNSKLMETLKEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3444444444554556666666666666666666654

>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens}

Probab=89.50  E-value=0.51  Score=32.56  Aligned_cols=31  Identities=19%  Similarity=0.406  Sum_probs=16.0

Q ss_pred             HHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          142 KINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       142 ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      ++..|+.|..+|+.+...|+.+++.|..+|.
T Consensus        20 d~eaLk~E~~eLk~k~~~L~~~~~el~~~l~   50 (53)
T 2yy0_A           20 EIELLRLELAEMKEKYEAIVEENKKLKAKLA   50 (53)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3444555555555555555555555555543

>3mq7_A Bone marrow stromal antigen 2; HIV, antiviral protein; 2.28A {Homo sapiens} PDB: 3mqc_A 3mqb_A 3mkx_A 3nwh_A 2xg7_A* 2x7a_A

Probab=89.39  E-value=1.8  Score=34.77  Aligned_cols=32  Identities=31%  Similarity=0.384  Sum_probs=17.3

Q ss_pred             HHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          142 KINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       142 ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .+++|+-|+..|..+.+..-+|+|+|..+...
T Consensus        72 ~vqeLqgEI~~Lnq~Lq~a~ae~erlr~~~~~  103 (121)
T 3mq7_A           72 KVEELEGEITTLNHKLQDASAEVERLRRENQV  103 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhchh
Confidence            35555555555555555555555555555443

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=89.07  E-value=3.4  Score=31.96  Aligned_cols=16  Identities=19%  Similarity=0.275  Sum_probs=7.3

Q ss_pred             HHHHHHHHHHHHHHHH
Q 026702          157 KQRLKNEKENLERQVK  172 (235)
Q Consensus       157 ~~~Lk~e~e~Le~qlk  172 (235)
                      ...++...++|+.||+
T Consensus        78 ~~~~e~kn~~L~~qL~   93 (97)
T 2eqb_B           78 KYAIEILNKRLTEQLR   93 (97)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            3344444444554444

>3v86_A De novo design helix; computational design of A protein crystal, helical coil, DE designed helix, de novo protein; 2.91A {Synthetic}

Probab=89.02  E-value=0.37  Score=28.87  Aligned_cols=26  Identities=35%  Similarity=0.450  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGKINEL  146 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~ei~~L  146 (235)
                      |+-+|+.++-+|+-+...|..|+++|
T Consensus         1 yvyqlkdevgelkgevralkdevkdl   26 (27)
T 3v86_A            1 YVYQLKDEVGELKGEVRALKDEVKDL   26 (27)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchhhHHHHHHHhHHHHHHHHHhcc
Confidence            44566666666666555555555544

>2ocy_A RAB guanine nucleotide exchange factor SEC2; RAB, GEF, guanine exchange factor, coiled-coil, endocytosis/exocytosis complex; 3.30A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=88.99  E-value=1.8  Score=35.98  Aligned_cols=23  Identities=17%  Similarity=0.225  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNE  137 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~  137 (235)
                      |..||++...|..++..++.+++
T Consensus         8 LI~Ain~qs~LeD~L~~~R~el~   30 (154)
T 2ocy_A            8 LIESVDKQSHLEEQLNKSLKTIA   30 (154)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHH
Confidence            45566666666665555555544

>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=88.64  E-value=0.66  Score=33.82  Aligned_cols=33  Identities=27%  Similarity=0.423  Sum_probs=22.3

Q ss_pred             HHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          143 INELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       143 i~~Lk~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            455666666666777777777777777776654

>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=88.46  E-value=1.9  Score=30.47  Aligned_cols=33  Identities=27%  Similarity=0.300  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKN  151 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~Ekn  151 (235)
                      ..|+.+|+.++..|+.+|..|..++..|+.+..
T Consensus        29 ~~~~~~Le~~v~~L~~eN~~L~~ev~~Lr~~l~   61 (63)
T 2dgc_A           29 LQRMKQLEDKVEELLSKNYHLENEVARLKKLVG   61 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            378888888888888888888777777766543

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=88.43  E-value=1.7  Score=40.64  Aligned_cols=53  Identities=21%  Similarity=0.251  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      ..|+.++.+|++..++|+.+++.++.+..++.++......+..+|..++..+.
T Consensus         6 ~~l~~el~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~rr~l~n~~~~l~   58 (412)
T 3u06_A            6 AALSTEVVHLRQRTEELLRCNEQQAAELETCKEQLFQSNMERKELHNTVMDLR   58 (412)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            46888888888888888888888888888888887777777777888887764

>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA complex, transcription factor, BZIP, C/EBP; 1.80A {Homo sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A 1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A

Probab=88.37  E-value=0.73  Score=34.18  Aligned_cols=33  Identities=27%  Similarity=0.378  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELR  154 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            344556666677777666666655555555443

>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=88.27  E-value=1.2  Score=31.97  Aligned_cols=37  Identities=24%  Similarity=0.372  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHH
Q 026702          126 RDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKN  162 (235)
Q Consensus       126 r~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~  162 (235)
                      +.++|+|-+-|..|.+|++.|..+++.|+.||..|+.
T Consensus        26 eAkiQQLmkVN~~ls~Elr~mQ~~lq~LQsen~~Lr~   62 (63)
T 2w6a_A           26 EAKVQQLMKVNSSLSDELRKLQREIHKLQAENLQLRQ   62 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhHhhhHHHHHHHHHHHHHHhhhhhhcc
Confidence            3567788888888888888888888888888888763

>3swf_A CGMP-gated cation channel alpha-1; coiled-coil, assembly domain, transport protein; 2.14A {Bos taurus}

Probab=88.11  E-value=1.7  Score=32.16  Aligned_cols=49  Identities=20%  Similarity=0.345  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          123 TQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      ++|++.|++|+..++.|+.....|-+|   +..-.++||+.+.+||.+++..
T Consensus         3 ~dlEEKv~~LE~sld~LQTrfARLLaE---y~ssQ~KLKqRit~LE~~~~~~   51 (74)
T 3swf_A            3 MGLEEKVTRMESSVDLLQTRFARILAE---YESMQQKLKQRLTKVEKFLKPL   51 (74)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhccc
Confidence            357888888888888888877666555   4455679999999999999973

>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=88.03  E-value=3.4  Score=38.88  Aligned_cols=77  Identities=12%  Similarity=0.082  Sum_probs=49.4

Q ss_pred             HHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702           90 LNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus        90 lNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~  169 (235)
                      +++.+..|....-++  .+ .+......++.+++.+..++.+|+..+..-.++|+.|+...+.++...+.|+.++..|+.
T Consensus        57 v~~Lvk~iq~~~~~~--Q~-~~~d~~e~~tq~skkml~~~~~~e~~~~~~~~~i~~l~~~~~~~~~~i~~l~~~i~~l~~  133 (409)
T 1m1j_C           57 IEYLIQHIKTIYPSE--KQ-TLPQSIEQLTQKSKKIIEEIIRYENTILAHENTIQQLTDMHIMNSNKITQLKQKIAQLES  133 (409)
T ss_dssp             HHHHHHHHHHHSCSS--TT-CCSSCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhcccc--cC-CCCCchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence            344455555555342  22 344555666999999999999998877777777777777776665555555555544443

>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=88.02  E-value=5.7  Score=28.88  Aligned_cols=57  Identities=11%  Similarity=0.193  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          117 DAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       117 dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .|.+-+.++...+...+.....+.+++..|+..+..|.++...+.......+..|..
T Consensus        17 ~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~ee~l~~a~~kLee   73 (81)
T 1ic2_A           17 NALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESLKDAQEKLEL   73 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555566666666666666666667666666666666666655555555555543

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=87.78  E-value=2.3  Score=36.73  Aligned_cols=53  Identities=8%  Similarity=0.055  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      -|..|+.++..++.....++.++.+++.++..+..+...++..+++.+.++..
T Consensus        33 el~~le~~~~~l~~~~~~~~~~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l~~   85 (256)
T 3na7_A           33 DLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMSE   85 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            34444444444444444555555555555555555555555555555555543

>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=87.75  E-value=3.1  Score=28.23  Aligned_cols=50  Identities=28%  Similarity=0.234  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702          118 AVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus       118 AI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      .-+++.++...+..++.+...+...++.+...++..+++...++.+++.+
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi~~y   59 (60)
T 3htk_A           10 LENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEYY   59 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34566677777777888888888888888888888888888888887753

>3u1c_A Tropomyosin alpha-1 chain; anti-parallel coiled coil, contractIle protein; 1.80A {Gallus gallus} PDB: 3u1a_A

Probab=87.70  E-value=5.2  Score=30.39  Aligned_cols=46  Identities=13%  Similarity=0.201  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHH
Q 026702          117 DAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKN  162 (235)
Q Consensus       117 dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~  162 (235)
                      .|++-..+++..+..++..+.++.+++..|...+..|.++...+..
T Consensus        20 ~a~drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~eld~~ee   65 (101)
T 3u1c_A           20 NALDRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTEDSRDQVLE   65 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566666666666666666666666666666655555555443333

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=87.68  E-value=5  Score=30.32  Aligned_cols=52  Identities=12%  Similarity=0.153  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702          116 ADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus       116 ~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      ..|++-..+++.++..++..+.++.+++..|+..+..|.++...+.......
T Consensus        19 e~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~eld~~~e~l~~a   70 (101)
T 3u59_A           19 ENAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEKYSESVKEA   70 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3566677777777777777777777777776666666666654444443333

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=87.56  E-value=3.6  Score=34.16  Aligned_cols=79  Identities=22%  Similarity=0.200  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHhhcCCCCC---CCCchhhhHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHhHhHHHHH
Q 026702           89 RLNDRFMELASILDPGRP---PKMDKTVLLADAVQMVTQLRDEAQKLK-------VSNEKLLGKINELKCEKNELRDEKQ  158 (235)
Q Consensus        89 klNd~F~~Lr~lLpP~~~---~K~dKasIL~dAI~yIk~Lr~~vq~Lk-------~~n~~L~~ei~~Lk~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 HLNELFQDNSGAIGG-NIVSHDDALL-NTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKLS  120 (152)
T ss_dssp             --------------C-HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhccCCCc-ccccchhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666666655533 10   01111 133333344555666665555       4466788888888888888888888


Q ss_pred             HHHHHHHHHHH
Q 026702          159 RLKNEKENLER  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            88888766544

>2wt7_B Transcription factor MAFB; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 2wty_A* 1k1v_A

Probab=87.48  E-value=1.5  Score=33.45  Aligned_cols=38  Identities=21%  Similarity=0.330  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          137 EKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       137 ~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      ..|+.+...|..+++.|+.|+..+..|++.+.+.++.+
T Consensus        51 ~~LE~e~~~L~~e~~~L~~e~~~~~~e~d~~k~k~~~L   88 (90)
T 2wt7_B           51 HHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKSEKL   88 (90)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44556666666666777777777777777777766654

>3swy_A Cyclic nucleotide-gated cation channel alpha-3; coiled-coil, assembly domain, transport protein; 1.90A {Homo sapiens}

Probab=87.33  E-value=2.4  Score=28.65  Aligned_cols=45  Identities=24%  Similarity=0.364  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~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 ALEEKVEQLGSSLDTLQTRFARLLAE---YNATQMKMKQRLSQLESQV   46 (46)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHhcC
Confidence            57778888888888888776666555   4445678899999998763

>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=86.86  E-value=1.2  Score=33.96  Aligned_cols=37  Identities=24%  Similarity=0.403  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Q 026702          130 QKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKEN  166 (235)
Q Consensus       130 q~Lk~~n~~L~~ei~~Lk~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            4455555555555555555555555555555554443

>3iv1_A Tumor susceptibility gene 101 protein; coiled_COIL, tumorigenesis, CELL_cycle regulation, alternative splicing, cell cycle, cell division; HET: MSE; 2.50A {Homo sapiens}

Probab=86.79  E-value=5.5  Score=29.64  Aligned_cols=45  Identities=27%  Similarity=0.367  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le  168 (235)
                      .|+..-+.|+.--.+|+.-+..|..|.++|......|+...+.|+
T Consensus        29 sLrrT~~EL~~G~~KL~~mi~~l~~E~~~l~~ni~~lk~K~~EL~   73 (78)
T 3iv1_A           29 ALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELS   73 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355666666666666766677777777777776666666665554

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=86.63  E-value=3.6  Score=32.15  Aligned_cols=52  Identities=15%  Similarity=0.123  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      |.-|+..+..+++.+..++.+.++..++.+.++.....|+.++..|+.||+.
T Consensus        32 VdlLKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~~lk~~L~q   83 (103)
T 4h22_A           32 VDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEVKEALKQ   83 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555666666666666666666666666666677777777777777776

>3swk_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural; 1.70A {Homo sapiens}

Probab=86.31  E-value=3.4  Score=30.72  Aligned_cols=36  Identities=11%  Similarity=0.221  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          139 LLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       139 L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      ++.++..|++..+++.--+..|..+++.|..+|.-+
T Consensus        47 ~E~d~~~LrkdvD~a~l~r~dLE~kvesL~eEl~fL   82 (86)
T 3swk_A           47 AENTLQSFRQDVDNASLARLDLERKVESLQEEIAFL   82 (86)
T ss_dssp             HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555566666666666777778888887777644

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=86.00  E-value=14  Score=30.96  Aligned_cols=80  Identities=20%  Similarity=0.258  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHH-HH
Q 026702           81 CREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEK-QR  159 (235)
Q Consensus        81 ~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~-~~  159 (235)
                      ..||+=|....+.+.+|-.-+              .....-|+.++....++..++..|++.+..|..|++.+.=+. =.
T Consensus        79 ~qEr~~r~q~se~~~elq~ri--------------~~L~~El~~~k~~~~k~~~e~r~L~Ekl~~lEKe~a~~eid~~~e  144 (168)
T 3o0z_A           79 EAERRDRGHDSEMIGDLQARI--------------TSLQEEVKHLKHNLEKVEGERKEAQDMLNHSEKEKNNLEIDLNYK  144 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Confidence            468888888888888887755              123345566677777788888888888888888888877443 46


Q ss_pred             HHHHHHHHHHHHHHh
Q 026702          160 LKNEKENLERQVKAL  174 (235)
Q Consensus       160 Lk~e~e~Le~qlk~~  174 (235)
                      ||+=-.++++++++.
T Consensus       145 LKalQ~~~eqE~~~H  159 (168)
T 3o0z_A          145 LKSLQQRLEQEVNEH  159 (168)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            777777888888774

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.68  E-value=1.3  Score=41.61  Aligned_cols=43  Identities=28%  Similarity=0.425  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 026702          137 EKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPA  179 (235)
Q Consensus       137 ~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~~~p~  179 (235)
                      .+|+.+++.|..|.+.+++|...++.|.++++.+++.+..+|.
T Consensus        52 k~le~~~~~L~~e~e~l~~~~~~~~~e~~~~~ee~~~l~~~~~   94 (428)
T 4b4t_K           52 KKLEKEYELLTLQEDYIKDEQRHLKRELKRAQEEVKRIQSVPL   94 (428)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSCE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence            3444445555556666667777777778888888888766663

>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=85.68  E-value=2.2  Score=31.39  Aligned_cols=42  Identities=12%  Similarity=0.166  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          130 QKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       130 q~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      .+|+.......+++......+.+|..+.+....++..|+.+|
T Consensus        22 ~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseL   63 (72)
T 3nmd_A           22 RDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNEL   63 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333334444444444444444444444

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=85.67  E-value=5.4  Score=29.72  Aligned_cols=31  Identities=13%  Similarity=0.228  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHhHhHHHHHHHHHHHHHHHH
Q 026702          139 LLGKINELKCEKNELRDEKQRLKNEKENLER  169 (235)
Q Consensus       139 L~~ei~~Lk~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            3333333444444333333333333333333

>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=85.42  E-value=7.4  Score=30.55  Aligned_cols=48  Identities=17%  Similarity=0.279  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          126 RDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       126 r~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ......|......|...+++|.....+..+.+..|.+++.+|++++..
T Consensus        68 EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~  115 (129)
T 2fxo_A           68 EERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSE  115 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444455566666666666666666667777777777666544

>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=85.26  E-value=1.4  Score=28.47  Aligned_cols=26  Identities=19%  Similarity=0.248  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702          123 TQLRDEAQKLKVSNEKLLGKINELKC  148 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L~~ei~~Lk~  148 (235)
                      +||..+|++|-.++..|+.++..|+.
T Consensus         4 nQLE~kVEeLl~~~~~Le~EV~RL~~   29 (36)
T 1kd8_A            4 KQLEAEVEEIESEVWHLENEVARLEK   29 (36)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            45555555555555554444444433

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=85.15  E-value=3  Score=28.65  Aligned_cols=31  Identities=16%  Similarity=0.205  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          141 GKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       141 ~ei~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      .-+.+|..+...|..||..|+.+++.|++++
T Consensus        22 ~~~~~LE~~v~~L~~eN~~L~~~~~~L~~~~   52 (55)
T 1dh3_A           22 EYVKSLENRVAVLENQNKTLIEELKALKDLY   52 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4466677777778888888888888777654

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=85.15  E-value=2.6  Score=30.98  Aligned_cols=51  Identities=14%  Similarity=0.040  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      |..++..|+....-+...|.+|...+-+.+.+...|+.++..|..+++.+.
T Consensus        12 le~Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L~~rl~~~~   62 (78)
T 3efg_A           12 LEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKVR   62 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            444445555544444444555555555555555555555555555555543

>3m48_A General control protein GCN4; leucine zipper, synthetic peptide, alpha helix, activa amino-acid biosynthesis, DNA-binding, nucleus; 1.45A {Synthetic} PDB: 3i1g_A 2ahp_A* 2o7h_A

Probab=85.03  E-value=1.1  Score=28.57  Aligned_cols=21  Identities=24%  Similarity=0.286  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 026702          124 QLRDEAQKLKVSNEKLLGKIN  144 (235)
Q Consensus       124 ~Lr~~vq~Lk~~n~~L~~ei~  144 (235)
                      ||+.+|++|-.+|..|+.|+.
T Consensus         4 QLE~kVEeLl~~n~~Le~EV~   24 (33)
T 3m48_A            4 QLEAKVEELLSKNWNLENEVA   24 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHHHHHHHH
Confidence            444444444444444444333

>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=84.68  E-value=2.2  Score=27.51  Aligned_cols=26  Identities=35%  Similarity=0.415  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELK  147 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk  147 (235)
                      ++||+..|++|..++..|+.++..|+
T Consensus         3 MnQLE~KVEeLl~~~~~Le~eV~RLk   28 (36)
T 1kd8_B            3 VKQLKAKVEELKSKLWHLKNKVARLK   28 (36)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            34555555555555444444444433

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=84.67  E-value=8.1  Score=30.40  Aligned_cols=42  Identities=24%  Similarity=0.373  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Q 026702          116 ADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEK  157 (235)
Q Consensus       116 ~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~  157 (235)
                      .++-.-|..|+.++..|...+..|+..+++|.+..+.|....
T Consensus        31 ~e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDLER~~   72 (111)
T 2v66_B           31 AQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAK   72 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHH
Confidence            344455566666666666666666666666666666555543

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=84.60  E-value=4.6  Score=31.92  Aligned_cols=23  Identities=26%  Similarity=0.494  Sum_probs=16.8

Q ss_pred             hHhHHHHHHHHHHHHHHHHHHHH
Q 026702          151 NELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       151 nELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ..+..|+..|..+++.|+.|+..
T Consensus        86 Ekl~~eKe~L~~ql~~Lq~q~~~  108 (110)
T 2v4h_A           86 EKLVEKKEYLQEQLEQLQREFNK  108 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHh
Confidence            45667788888888888877654

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=84.50  E-value=4.9  Score=36.88  Aligned_cols=31  Identities=16%  Similarity=0.274  Sum_probs=15.7

Q ss_pred             HHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          142 KINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       142 ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      +.+....+.+.|++|+.+|+.+++.+..++.
T Consensus       436 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  466 (487)
T 3oja_A          436 DWDMYQHKETQLAEENARLKKLNGEADLALA  466 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhHHHHHHHHhhhhhhhhhhhhhhhH
Confidence            3444444445555555555555555555444

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=84.02  E-value=22  Score=32.49  Aligned_cols=52  Identities=8%  Similarity=0.004  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .++++.+..++++..+..+++++.|+.|++.++.+...+..+++...+.++.
T Consensus       423 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  474 (487)
T 3oja_A          423 YVEQQSVQNNAIRDWDMYQHKETQLAEENARLKKLNGEADLALASANATLQE  474 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcchhhhhhhhhHHHHHHHHhhhhhhhhhhhhhhhHhcccHHHH
Confidence            3334444444455666677778888888888888888777777777766654

>3vmx_A Voltage-gated hydrogen channel 1; coiled-coil, ION channel, ION transport, membrane protein; 1.45A {Mus musculus}

Probab=83.66  E-value=3.3  Score=28.33  Aligned_cols=41  Identities=27%  Similarity=0.275  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          127 DEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       127 ~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      .++.+|++.|..|-..|.+|....       ..+.+||++|..-|+..
T Consensus         4 q~l~kLKe~n~~L~~kv~~Le~~c-------~~~eQEieRL~~LLkqH   44 (48)
T 3vmx_A            4 RQILRLKQINIQLATKIQHLEFSC-------SEKEQEIERLNKLLKQN   44 (48)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHc-------cHHHHHHHHHHHHHHHc
Confidence            466788888888876665554444       44556888888877763

>1lwu_C Fibrinogen gamma chain; heterotrimer, protein-peptide complex, blood clotting; HET: NDG MAN NAG BMA GAL; 2.80A {Petromyzon marinus} SCOP: d.171.1.1 h.1.8.1 PDB: 1n73_C*

Probab=83.39  E-value=2.7  Score=38.41  Aligned_cols=54  Identities=15%  Similarity=0.120  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk  172 (235)
                      +.=++.|+.++.+|+..+....++|+.|+.....++...+.|+.++..|+..+.
T Consensus         4 ~~~~~~~~~~~~~~e~~i~~~~~~i~~L~~~l~~~~~~i~~l~~~i~~l~~~~~   57 (323)
T 1lwu_C            4 QKTVQKILEEVRILEQIGVSHDAQIQELSEMWRVNQQFVTRLQQQLVDIRQTCS   57 (323)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            334555666666666666666666666666666666666666666666655443

>1wt6_A Myotonin-protein kinase; coiled-coil, kinase activation, DMPK, molecular replacement, transferase; 1.60A {Homo sapiens}

Probab=83.19  E-value=10  Score=28.43  Aligned_cols=27  Identities=11%  Similarity=0.229  Sum_probs=14.2

Q ss_pred             HHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          147 KCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       147 k~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      ..+..+....|..|..|+++|+.+++.
T Consensus        44 eskL~eae~rn~eL~~e~~~l~~~~ee   70 (81)
T 1wt6_A           44 ASQLREAEARNRDLEAHVRQLQERMEL   70 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444455555566666665555

>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=83.05  E-value=5.1  Score=34.47  Aligned_cols=51  Identities=20%  Similarity=0.255  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      +++.-+-..++.++.+|..|..+...|..+.++|..+...+-.+|+.+|.+
T Consensus       125 elfd~~~~~~~~~~~~~~~L~~e~~~l~~~~~~l~~qlE~~v~~K~~~E~~  175 (213)
T 1ik9_A          125 ELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETD  175 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444555555555555555555555555555544444444444443

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=83.03  E-value=6.1  Score=34.04  Aligned_cols=16  Identities=6%  Similarity=-0.049  Sum_probs=5.8

Q ss_pred             HHHHHHHHHHHHHHHH
Q 026702          126 RDEAQKLKVSNEKLLG  141 (235)
Q Consensus       126 r~~vq~Lk~~n~~L~~  141 (235)
                      +.++.+++.+...+..
T Consensus        59 ~~~~~~~e~~i~~~~~   74 (256)
T 3na7_A           59 KLQVSKNEQTLQDTNA   74 (256)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3333333333333333

>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=83.01  E-value=10  Score=28.22  Aligned_cols=49  Identities=22%  Similarity=0.242  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          126 RDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       126 r~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      +.+++.|+.+.+.|..--..|..-+++|.+|...|...++.|+...+.+
T Consensus        24 qaEl~sLrrT~~EL~~G~~KL~~mi~~l~~E~~~l~~ni~~lk~K~~EL   72 (78)
T 3iv1_A           24 QAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEEL   72 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555554445555556666666666766676666655544

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=82.86  E-value=4  Score=30.02  Aligned_cols=48  Identities=6%  Similarity=0.046  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLE  168 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le  168 (235)
                      .|.+|+.++.=++...+.|...+-.-..++..|+.+...|...+..++
T Consensus        15 Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L~~rl~~~~   62 (78)
T 3efg_A           15 RLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKVR   62 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            455555555555555555555555555555555555555555444444

>2oxj_A Hybrid alpha/beta peptide based on the GCN4-P1 Se heptad positions B and F substituted...; helix bundle, foldamer, unknown function; HET: B3K B3D B3E B3S B3Y B3X B3A BAL; 2.00A {Synthetic} PDB: 2oxk_A*

Probab=82.80  E-value=1.9  Score=27.48  Aligned_cols=21  Identities=24%  Similarity=0.292  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 026702          123 TQLRDEAQKLKVSNEKLLGKI  143 (235)
Q Consensus       123 k~Lr~~vq~Lk~~n~~L~~ei  143 (235)
                      .||+.+|++|-.+|+.|+.++
T Consensus         4 nQLE~kVEeLl~~n~~Le~eV   24 (34)
T 2oxj_A            4 XQLEXKVXELLXKNXHLEXEV   24 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhHHHHH
Confidence            344444444444444443333

>2w83_C C-JUN-amino-terminal kinase-interacting protein 4; golgi apparatus, protein transport, ER-golgi transport, ARF, GTPase, effector, myristate; HET: GTP; 1.93A {Homo sapiens}

Probab=82.75  E-value=9.5  Score=28.37  Aligned_cols=35  Identities=37%  Similarity=0.640  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          139 LLGKINELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       139 L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      |-..+.+|..|+.-|+.|+..++.-+.|++..++.
T Consensus        35 LI~rvdELt~E~e~l~~El~s~~~~~~r~~~ri~e   69 (77)
T 2w83_C           35 LIAKVDELTCEKDVLQGELEAVKQAKLKLEEKNRE   69 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44456666666666666666666666666665554

>2j5u_A MREC protein; bacterial cell shape determining protein MREC, cell shape regulation; 2.5A {Listeria monocytogenes}

Probab=82.68  E-value=0.45  Score=41.66  Aligned_cols=15  Identities=27%  Similarity=0.508  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHH
Q 026702          159 RLKNEKENLERQVKA  173 (235)
Q Consensus       159 ~Lk~e~e~Le~qlk~  173 (235)
                      .|+.|.++|+..|..
T Consensus        47 ~l~~En~rLr~lL~~   61 (255)
T 2j5u_A           47 DLKKENKDLKESLDI   61 (255)
T ss_dssp             HHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhcC
Confidence            445555566665554

>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus norvegicus}

Probab=82.49  E-value=5.8  Score=30.03  Aligned_cols=11  Identities=0%  Similarity=0.232  Sum_probs=3.9

Q ss_pred             HHHHHHHHHHH
Q 026702          138 KLLGKINELKC  148 (235)
Q Consensus       138 ~L~~ei~~Lk~  148 (235)
                      .|..+|..++.
T Consensus        36 ~l~~el~~le~   46 (96)
T 3q8t_A           36 VVAENLEKVQA   46 (96)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            33333333333

>2oxj_A Hybrid alpha/beta peptide based on the GCN4-P1 Se heptad positions B and F substituted...; helix bundle, foldamer, unknown function; HET: B3K B3D B3E B3S B3Y B3X B3A BAL; 2.00A {Synthetic} PDB: 2oxk_A*

Probab=82.31  E-value=2.5  Score=26.96  Aligned_cols=25  Identities=36%  Similarity=0.461  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHhHhHHHHHHHH
Q 026702          137 EKLLGKINELKCEKNELRDEKQRLK  161 (235)
Q Consensus       137 ~~L~~ei~~Lk~EknELr~E~~~Lk  161 (235)
                      .+|+.++++|-.++++|++|..+|+
T Consensus         4 nQLE~kVEeLl~~n~~Le~eV~rLk   28 (34)
T 2oxj_A            4 XQLEXKVXELLXKNXHLEXEVXRLK   28 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            4555666666666666666555554

>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=82.02  E-value=2.8  Score=31.18  Aligned_cols=29  Identities=28%  Similarity=0.445  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702          139 LLGKINELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus       139 L~~ei~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      |+.+...+..++++|+.++..|+.+++.|
T Consensus        57 L~~~~~~l~~~~~~L~~~n~~L~~rl~~L   85 (88)
T 1nkp_A           57 VQAEEQKLISEEDLLRKRREQLKHKLEQL   85 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33333334444444555555555444443

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=81.87  E-value=13  Score=29.05  Aligned_cols=23  Identities=26%  Similarity=0.410  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGK  142 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~e  142 (235)
                      +-|..|+.+++.|+..+..|+..
T Consensus        43 r~iq~L~~el~~l~~~~~~LE~~   65 (129)
T 3tnu_B           43 RMIQRLRAEIDNVKKQCANLQNA   65 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHH
Confidence            33444444444444444444443

>1fxk_C Protein (prefoldin); archaeal protein, chaperone; 2.30A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: a.2.5.1

Probab=81.86  E-value=5.3  Score=30.90  Aligned_cols=43  Identities=14%  Similarity=0.268  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHH
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRL  160 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~L  160 (235)
                      +.+|++|   |..+++.|+...+.|+..+..++.+.+.+.++...+
T Consensus        86 ~~eA~~~---l~~r~~~l~~~~~~l~~~l~~l~~~i~~~~~~l~~~  128 (133)
T 1fxk_C           86 FEDAMES---IKSQKNELESTLQKMGENLRAITDIMMKLSPQAEEL  128 (133)
T ss_dssp             HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5677777   556667777776666666666666666655544443

>3trt_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural protein; 2.30A {Homo sapiens} PDB: 3klt_A*

Probab=81.83  E-value=5.4  Score=28.31  Aligned_cols=25  Identities=32%  Similarity=0.392  Sum_probs=12.7

Q ss_pred             HHHHHHHHhHhHHHHHHHHHHHHHH
Q 026702          143 INELKCEKNELRDEKQRLKNEKENL  167 (235)
Q Consensus       143 i~~Lk~EknELr~E~~~Lk~e~e~L  167 (235)
                      +...+.|+.|||...+.|..|++.|
T Consensus        51 l~~~k~Ei~elrr~iq~L~~el~sl   75 (77)
T 3trt_A           51 LRQAKQESTEYRRQVQSLTMEVDAL   75 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3444555555555555555555443

>3ni0_A Bone marrow stromal antigen 2; coiled-coil, antiviral defense, immune system, GPI anchor; 1.60A {Mus musculus}

Probab=81.42  E-value=15  Score=28.47  Aligned_cols=60  Identities=17%  Similarity=0.223  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          115 LADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       115 L~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      |+.|-+.+.+-+.++.--......|..-.+.-+..-.+-+.....|+.||..|.++|+..
T Consensus        27 LT~Aq~~l~~~eaQAaTCNqTV~tL~~SL~kekaq~q~qq~~v~elqgEI~~Lnq~Lqda   86 (99)
T 3ni0_A           27 LTRTQDSLLQAETQANSCNLTVVTLQESLEKKVSQALEQQARIKELENEVTKLNQELENL   86 (99)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444333344444543332222222222344667777888888877764

>2zvf_A Alanyl-tRNA synthetase; C-terminal, oligomerization domain, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase, nucleotide-binding; 3.20A {Archaeoglobus fulgidus}

Probab=81.42  E-value=2.2  Score=34.09  Aligned_cols=22  Identities=18%  Similarity=0.175  Sum_probs=9.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 026702          121 MVTQLRDEAQKLKVSNEKLLGK  142 (235)
Q Consensus       121 yIk~Lr~~vq~Lk~~n~~L~~e  142 (235)
                      -|..|++++.+|++++++|+.+
T Consensus        33 ~v~~l~~e~k~l~ke~~~l~~~   54 (171)
T 2zvf_A           33 TVERFFEEWKDQRKEIERLKSV   54 (171)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444433

>1jcd_A Major outer membrane lipoprotein; protein folding, coiled coil, helix capping, alanine-zipper, membrane protein; 1.30A {Escherichia coli} SCOP: h.1.16.1 PDB: 1eq7_A 1t8z_A* 2guv_A 2gus_A 1jcc_A 1kfn_A 1kfm_A

Probab=81.33  E-value=6.1  Score=27.21  Aligned_cols=31  Identities=13%  Similarity=0.203  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCEKNE  152 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~EknE  152 (235)
                      |.+|-.+|+.|......|..++..|+.+...
T Consensus         6 i~~Lss~V~~L~~kVdqLssdV~al~~~v~~   36 (52)
T 1jcd_A            6 ADQASSDAQTANAKADQASNDANAARSDAQA   36 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666666666666665555555544443

>3bas_A Myosin heavy chain, striated muscle/general control protein GCN4 chimera; alpha-helical coiled coil, disorder, salt links; 2.30A {Argopecten irradians} SCOP: h.1.26.1 PDB: 1nkn_A 3bat_A

Probab=81.29  E-value=14  Score=27.30  Aligned_cols=37  Identities=30%  Similarity=0.390  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHh
Q 026702          138 KLLGKINELKCEKNELRDEKQRLKNEKENLERQVKAL  174 (235)
Q Consensus       138 ~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~~  174 (235)
                      +|.++...|..+..+..+....|.+.+-.|+.+|+.+
T Consensus        46 ~l~~ek~~L~~ql~eaEe~~~~L~~~K~eLE~~l~el   82 (89)
T 3bas_A           46 TLLEQKNDLFGSMKQLEDKVEELLSKNYHLENEVARL   82 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333334444555566666666777776654

>2w83_C C-JUN-amino-terminal kinase-interacting protein 4; golgi apparatus, protein transport, ER-golgi transport, ARF, GTPase, effector, myristate; HET: GTP; 1.93A {Homo sapiens}

Probab=81.13  E-value=8.5  Score=28.64  Aligned_cols=46  Identities=28%  Similarity=0.244  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHH
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQ  170 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~q  170 (235)
                      |-.+..+|..+...|.---++|-+..+||.-|+..|+.|++.+++-
T Consensus        14 Li~EN~eLl~TKNaLnvvk~DLI~rvdELt~E~e~l~~El~s~~~~   59 (77)
T 2w83_C           14 LILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQA   59 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            3333344444333343334556666667777777777777766653

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=81.12  E-value=8.5  Score=30.09  Aligned_cols=28  Identities=11%  Similarity=0.272  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINELKCE  149 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~Lk~E  149 (235)
                      |.+|+..++.|+.+++.|+.....|...
T Consensus        38 i~elrr~iq~L~~el~~l~~~~~~LE~~   65 (129)
T 3tnu_B           38 ISEMNRMIQRLRAEIDNVKKQCANLQNA   65 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            4444444444444444444444444433

>1uix_A RHO-associated kinase; coiled-coil, transferase; HET: MSE; 1.80A {Bos taurus} SCOP: h.1.27.1

Probab=80.96  E-value=9.4  Score=27.93  Aligned_cols=46  Identities=24%  Similarity=0.343  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Q 026702          126 RDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQV  171 (235)
Q Consensus       126 r~~vq~Lk~~n~~L~~ei~~Lk~EknELr~E~~~Lk~e~e~Le~ql  171 (235)
                      ...++.|..+++.|...++.+..+...+++|-......+.+|+.+|
T Consensus         3 ~k~v~~l~~E~eel~~klk~~~ee~~~~~eee~~~~~~k~~lek~L   48 (71)
T 1uix_A            3 TSDVANLANEKEELNNKLKEAQEQLSRLKDEEISAAAIKAQFEKQL   48 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444445554444444444444444444444333444444443

>3ibp_A Chromosome partition protein MUKB; structural maintenance of chromosomes, SMC, condensin, chromosome segregation, hinge, dimerization domain; 3.10A {Escherichia coli}

Probab=80.68  E-value=11  Score=34.30  Aligned_cols=76  Identities=21%  Similarity=0.291  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHH-------HHHHHHH-HHHHHHHHHHHHHHhHh
Q 026702           82 REKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEA-------QKLKVSN-EKLLGKINELKCEKNEL  153 (235)
Q Consensus        82 ~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~v-------q~Lk~~n-~~L~~ei~~Lk~EknEL  153 (235)
                      .-|.+++.|+..+..|.+.- |          +-..|-.-+.+|+.+.       +.+-... ..|..| ++++.+++++
T Consensus        21 ~lr~~~eql~~~i~~L~~~a-p----------~W~~aq~al~rL~eq~g~~~~ds~~v~~~mq~~Le~E-re~~~~Rd~~   88 (302)
T 3ibp_A           21 ALRQEQEQLQSRIQSLMQRA-P----------VWLAAQNSLNQLSEQCGEEFTSSQDVTEYLQQLLERE-REAIVERDEV   88 (302)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH-H----------HHHHHHHHHHHHHHHTTCCCSSHHHHHHHHHHHHHHH-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHC-h----------HHHHHHHHHHHHHHHhCCcCCCHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence            45667788888888887776 3          3344555555566653       3443333 344444 7788888888


Q ss_pred             HHHHHHHHHHHHHHHH
Q 026702          154 RDEKQRLKNEKENLER  169 (235)
Q Consensus       154 r~E~~~Lk~e~e~Le~  169 (235)
                      -..+..|..+|++|-+
T Consensus        89 a~~k~~Le~~ierLs~  104 (302)
T 3ibp_A           89 GARKNAVDEEIERLSQ  104 (302)
T ss_dssp             HHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHcC
Confidence            8888888888888776

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=80.52  E-value=1.6  Score=34.44  Aligned_cols=55  Identities=15%  Similarity=0.107  Sum_probs=15.7

Q ss_pred             HHHHHHHHhhcCCCCC-CCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           91 NDRFMELASILDPGRP-PKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINEL  146 (235)
Q Consensus        91 Nd~F~~Lr~lLpP~~~-~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~L  146 (235)
                      +.+|.+|...+..... -+..|.. |.+.-+-|..|+.+++.++..+..|+..+.++
T Consensus        16 ~~K~eel~~~~~~~~~~l~~~k~E-i~elrr~iq~L~~el~~l~~~~~sLE~~l~e~   71 (131)
T 3tnu_A           16 FTKTEELNREVATNSELVQSGKSE-ISELRRTMQNLEIELQSQLSMKASLENSLEET   71 (131)
T ss_dssp             --------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            3456667766622110 0111211 33334445555555555555555555544433

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

Probab=80.19  E-value=4.5  Score=29.64  Aligned_cols=17  Identities=29%  Similarity=0.575  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 026702          155 DEKQRLKNEKENLERQV  171 (235)
Q Consensus       155 ~E~~~Lk~e~e~Le~ql  171 (235)
                      .|+..|+.+.+.|+++|
T Consensus        61 ~e~~~L~~e~~~L~~~L   77 (80)
T 1nlw_A           61 HQIDQLQREQRHLKRQL   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            33333333333333333

>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}

Probab=80.10  E-value=7.9  Score=37.18  Aligned_cols=52  Identities=23%  Similarity=0.359  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH------------------HHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKINEL------------------KCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei~~L------------------k~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      -++|+.+++.|+.+...+..+|..+                  +.+..+|+++...|+.+...++.+|..
T Consensus        79 ~r~~~~~~~~l~~~rn~~sk~i~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~~~~~l~~  148 (501)
T 1wle_A           79 LRQLREQIRSLEEEKEAVTEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQLEEQFYL  148 (501)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTGGGCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555666665555555445444                  344444444444444455555555544

>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=80.04  E-value=8.8  Score=29.95  Aligned_cols=52  Identities=25%  Similarity=0.220  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-------HHhHhHHHHHHHHHHHHHHHHHHHHhcC
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKC-------EKNELRDEKQRLKNEKENLERQVKALSS  176 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~-------EknELr~E~~~Lk~e~e~Le~qlk~~~~  176 (235)
                      |-.+-=.|+...+.|+++.+.|+.       .+.+|..|..+|+.|..+|.++-+.+..
T Consensus        35 LIqEYl~LE~~~s~le~e~~rlr~~~~~~~~~v~eLe~everL~~ENq~L~~e~~~~~~   93 (104)
T 3s9g_A           35 LIKEYLELEKSLSRMEDENNRLRLESKRLDARVRELELELDRLRAENLQLLTENELHRQ   93 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            334444667777777777777776       4556777777777777777777666543

>2oto_A M protein; helical coiled coil, fibrinogen-binding, virulence factor, S active protein, toxin; 3.04A {Streptococcus pyogenes serotype M1} PDB: 2xny_M

Probab=80.03  E-value=8.1  Score=31.04  Aligned_cols=25  Identities=28%  Similarity=0.369  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702          125 LRDEAQKLKVSNEKLLGKINELKCE  149 (235)
Q Consensus       125 Lr~~vq~Lk~~n~~L~~ei~~Lk~E  149 (235)
                      |..+++.|+..|..|+.+.++++.+
T Consensus        55 L~~~~~~Le~~n~~L~~~lke~~~~   79 (155)
T 2oto_A           55 LEKAKQALEDQRKDLETKLKELQQD   79 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444333333

---

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	8e-17
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	1e-13
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	2e-13
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	2e-12
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	1e-11
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	6e-09
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	2e-08
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	3e-06
d2ap3a1	185	a.24.27.1 (A:12-196) Hypothetical protein MW0975 (	7e-04
d2elba1	268	a.238.1.1 (A:6-273) DCC-interacting protein 13-alp	0.003

>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 = 70.7 bits (173), Expect = 8e-17
 Identities = 14/73 (19%), Positives = 29/73 (39%)

Query: 82  REKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLG 141
            E+ RRD + D F  L   +   +  K  +  +L  A + +  +R +    +   + L  
Sbjct: 9   LERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR 68

Query: 142 KINELKCEKNELR 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 = 62.2 bits (151), Expect = 1e-13
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 82  REKMRRDRLNDRFMELASIL-DPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLL 140
            E+ RR+ L   F  L   + +     K  K V+L  A   +  ++ E QKL    + L 
Sbjct: 13  LERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR 72

Query: 141 GKINELKCEKNELR 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 = 61.9 bits (150), Expect = 2e-13
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 82  REKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLG 141
            EK  R  +ND+ +EL   L  G   K++K+ +L  A+  +  L+   QKLK  N  L  
Sbjct: 13  IEKRYRSSINDKIIELKD-LVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT 71

Query: 142 KINELKCEK 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 = 59.1 bits (143), Expect = 2e-12
 Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 82  REKMRRDRLNDRFMELASILDPGRP-PKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLL 140
            EK RR  L     +L  ++  G    +     LL  A   + +L D  +K     ++L 
Sbjct: 8   MEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ 67

Query: 141 GKINELK 147
            +   LK
Sbjct: 68  REQRHLK 74

>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 = 55.9 bits (135), Expect = 1e-11
 Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 87  RDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKL 139
           R  +ND+ +EL  ++  G   KM K+ +L  A+  +  L+    KL+  N  L
Sbjct: 1   RSSINDKIIELKDLV-MGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVL 52

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (117), Expect = 6e-09
 Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 82  REKMRRDRLNDRFMELASIL----DPGRPPKMDKTVLLADAVQMVTQLRDEAQK 131
            E+ RRD++N+  ++L+ I+             K  +L+ 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 = 47.6 bits (113), Expect = 2e-08
 Identities = 10/66 (15%), Positives = 28/66 (42%)

Query: 65  RKRVRSGSCSASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQ 124
             + ++ +     +   RE+ R  ++N+ F  L          ++ K  +L +A++ +  
Sbjct: 2   ELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEG 61

Query: 125 LRDEAQ 130
           L+   +
Sbjct: 62  LQALLR 67

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 63

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.4 bits (97), Expect = 3e-06
 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 5/54 (9%)

Query: 82  REKMRRDRLNDRFMELASIL-----DPGRPPKMDKTVLLADAVQMVTQLRDEAQ 130
            E+ RR+RL     ELAS++              K   +  A + +  L+    
Sbjct: 9   AEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

>d2ap3a1 a.24.27.1 (A:12-196) Hypothetical protein MW0975 (SA0943) {Staphylococcus aureus [TaxId: 1280]} Length = 185

class: All alpha proteins
fold: Four-helical up-and-down bundle
superfamily: MW0975(SA0943)-like
family: MW0975(SA0943)-like
domain: Hypothetical protein MW0975 (SA0943)
species: Staphylococcus aureus [TaxId: 1280]

 Score = 37.0 bits (84), Expect = 7e-04
 Identities = 9/87 (10%), Positives = 30/87 (34%)

Query: 82  REKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLG 141
            ++    +L+D   E   +                   + + Q     Q +   ++ +  
Sbjct: 99  VKRKEVKQLDDVLKEKYKLHSDYAKAYKKAVNSEKTLFKYLNQNDATQQGVNEKSKAIEQ 158

Query: 142 KINELKCEKNELRDEKQRLKNEKENLE 168
              +LK   ++      +++ EK++++
Sbjct: 159 NYKKLKEVSDKYTKVLNKVQKEKQDVD 185

>d2elba1 a.238.1.1 (A:6-273) DCC-interacting protein 13-alpha, APPL1 {Human (Homo sapiens) [TaxId: 9606]} Length = 268

class: All alpha proteins
fold: BAR/IMD domain-like
superfamily: BAR/IMD domain-like
family: BAR domain
domain: DCC-interacting protein 13-alpha, APPL1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 11/69 (15%), Positives = 29/69 (42%), Gaps = 3/69 (4%)

Query: 124 QLRDEAQKLKVSNEKLLGKINELKCEKNELRDEKQRLKNEKENLERQVKALSSQPAFLPH 183
           Q+       +  NE+L   +  +      +++ ++ + ++ E +++ ++ L      L  
Sbjct: 202 QISFFKMGSENLNEQLEEFLANIG---TSVQNVRREMDSDIETMQQTIEDLEVASDPLYV 258

Query: 184 PPPVPAPFS 192
           P P P  F 
Sbjct: 259 PDPDPTDFP 267

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
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.73
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.73
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.72
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.56
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.55
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.53
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.45
d1lrza1	65	Methicillin resistance protein FemA probable tRNA-	87.63
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	86.56
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	86.12

>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=128.65  Aligned_cols=79  Identities=18%  Similarity=0.253  Sum_probs=67.1

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHh
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNEL  153 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            3568999999999999999999999996444579999999999999999999999998888777776666666665554

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=3.1e-18  Score=126.09  Aligned_cols=72  Identities=28%  Similarity=0.423  Sum_probs=64.3

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELK  147 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk  147 (235)
                      ++.+|+.+||+||++||+.|.+|+++| |+...|+||++||..||+||++|+.+++.|+.++..|+.++..++
T Consensus         6 kR~~H~~~Er~RR~~in~~~~~L~~ll-P~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~~~~~~   77 (80)
T d1am9a_           6 KRTAHNAIEKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH-TCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            467899999999999999999999999 556689999999999999999999999999998888877665543

>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=5.3e-18  Score=124.15  Aligned_cols=76  Identities=21%  Similarity=0.235  Sum_probs=65.6

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHHhhcCCCC-CCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026702           76 SGSKACREKMRRDRLNDRFMELASILDPGR-PPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKN  151 (235)
Q Consensus        76 ~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~-~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~Ekn  151 (235)
                      +..|+.+||+||++||++|.+|+++||++. ..|++|++||..||+||++|+.+++.|..+.+.|..+...|+.+.+
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~~~~~L~~~l~   78 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLE   78 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            457999999999999999999999996543 4689999999999999999999999988888888777766666543

>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=6.4e-18  Score=125.96  Aligned_cols=79  Identities=24%  Similarity=0.322  Sum_probs=66.2

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCC-CCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHh
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPG-RPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKINELKCEKNEL  153 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~-~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~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            456899999999999999999999999543 2368999999999999999999999988887777766666666665554

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.4e-15  Score=106.96  Aligned_cols=56  Identities=29%  Similarity=0.415  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026702           87 RDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQKLKVSNEKLLGKI  143 (235)
Q Consensus        87 RdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq~Lk~~n~~L~~ei  143 (235)
                      |++||++|.+|+++| |+...|+|||+||.+||+||++|+++++.|+.++..|+.+.
T Consensus         1 R~~in~~f~~L~~lv-P~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~   56 (61)
T d1uklc_           1 RSSINDKIIELKDLV-MGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLAN   56 (61)
T ss_dssp             CCCHHHHHHHHHHHH-SCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhC-CCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999 65557999999999999999999999999999988887653

>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=99.55  E-value=1.4e-15  Score=107.41  Aligned_cols=55  Identities=24%  Similarity=0.332  Sum_probs=49.1

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCC-----CCCCCCchhhhHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDP-----GRPPKMDKTVLLADAVQMVTQLRDEA  129 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP-----~~~~K~dKasIL~dAI~yIk~Lr~~v  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            46789999999999999999999999953     23579999999999999999998764

>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=99.53  E-value=8e-16  Score=110.46  Aligned_cols=57  Identities=18%  Similarity=0.307  Sum_probs=50.8

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHH
Q 026702           74 SASGSKACREKMRRDRLNDRFMELASILDPGRPPKMDKTVLLADAVQMVTQLRDEAQ  130 (235)
Q Consensus        74 ~~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~~~~K~dKasIL~dAI~yIk~Lr~~vq  130 (235)
                      .++..|+.+||+||++||+.|.+|+++||+....|+||++||..||+||++|++.++
T Consensus        11 ~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          11 DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            467889999999999999999999999965445689999999999999999997654

>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=99.45  E-value=1.2e-14  Score=102.99  Aligned_cols=55  Identities=22%  Similarity=0.369  Sum_probs=48.5

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHhhcCCC----CCCCCchhhhHHHHHHHHHHHHHHH
Q 026702           75 ASGSKACREKMRRDRLNDRFMELASILDPG----RPPKMDKTVLLADAVQMVTQLRDEA  129 (235)
Q Consensus        75 ~~~~h~~~ERrRRdklNd~F~~Lr~lLpP~----~~~K~dKasIL~dAI~yIk~Lr~~v  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            567899999999999999999999999542    2359999999999999999998654

>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=87.63  E-value=1.9  Score=29.23  Aligned_cols=53  Identities=17%  Similarity=0.260  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHhHhHHHHHHHHHHHHHHHHHHH
Q 026702          120 QMVTQLRDEAQKLKVSNEKLLGKI------NELKCEKNELRDEKQRLKNEKENLERQVK  172 (235)
Q Consensus       120 ~yIk~Lr~~vq~Lk~~n~~L~~ei------~~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            799999999999999998887664      33555566666666666666666555444

>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=86.56  E-value=2.3  Score=30.31  Aligned_cols=52  Identities=19%  Similarity=0.376  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHhHhHHHHHHHHHHHHHHHHHHHH
Q 026702          122 VTQLRDEAQKLKVSNEKLLGKI--------NELKCEKNELRDEKQRLKNEKENLERQVKA  173 (235)
Q Consensus       122 Ik~Lr~~vq~Lk~~n~~L~~ei--------~~Lk~EknELr~E~~~Lk~e~e~Le~qlk~  173 (235)
                      .++|+.+++.|+.+...+-.+|        .+|..+..+|.++...|..+...++.++..
T Consensus        37 rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~~~l~~   96 (110)
T d1seta1          37 VQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEA   96 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555544444333        334444444555555555555555555555

>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=86.12  E-value=4.3  Score=28.81  Aligned_cols=57  Identities=19%  Similarity=0.233  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--------HhHHHHHHHHHHHHHHHHHHHHhc
Q 026702          119 VQMVTQLRDEAQKLKVSNEKLLGKINELKCEKN--------ELRDEKQRLKNEKENLERQVKALS  175 (235)
Q Consensus       119 I~yIk~Lr~~vq~Lk~~n~~L~~ei~~Lk~Ekn--------ELr~E~~~Lk~e~e~Le~qlk~~~  175 (235)
                      ++.|-.|-.+..++..+.+.|+.+.+.+..++.        +|..+...|+.++..|+.+++.+.
T Consensus        27 ld~i~~ld~~rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~   91 (110)
T d1seta1          27 LEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKE   91 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666777777777777777777766665552        334444566666666666666543