Citrus Sinensis ID: 032660

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130------
Protein Sequence
MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Secondary Structure (PSIPRED)
cccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccc
Coil and Loop (DISEMBL)
mlepgrppktdkatILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAmsapsgflphpssmsAAFAAQSQVAsnklvpfigypgvamwqfmppaavdtsqdhvlrppva
Flexible Loop (DISEMBL)
mlepgrppktdkatilsDVVRMMEQLRTEAQKLKQSTEDLQEKIKELkaeknelrdeKQRLKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Low Complexity Region (SEG)
MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPssmsaafaaqsqvasNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Disordered region (IsUnstruct)
**************************************************************************************************ASNKLVPFIGYPGVAMWQFMPPA***************
Disordered Region (DISOPRED)
**E**R*PKTDKATILSDVVRMMEQLRTEA**************************************************************************PFIGYPGVAMWQFMPPA****SQ****RPP**
Disordered Region (DISEMBL)
***********KATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Disordered Region (DISPRO)
****GRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPPAAVD****HVLRPP**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLEPGRPPKTDKATIxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA
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	136	2.2.26 [Sep-21-2011]
Q9FH37	234	Transcription factor ILR3	yes	no	1.0	0.581	0.739	2e-51
Q9C682	226	Transcription factor bHLH	no	no	0.963	0.579	0.635	2e-43
Q8L467	283	Transcription factor bHLH	no	no	0.933	0.448	0.540	3e-32
Q9LTC7	320	Transcription factor bHLH	no	no	0.948	0.403	0.507	8e-28
Q9LT23	337	Transcription factor bHLH	no	no	0.610	0.246	0.420	3e-10
Q8W2F2	286	Transcription factor bHLH	no	no	0.727	0.346	0.376	3e-08

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

 Score =  200 bits (508), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 102/138 (73%), Positives = 110/138 (79%), Gaps = 2/138 (1%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPG PPKTDKA IL D VRM+ QLR EAQKLK S   LQ+KIKELK EKNELRDEKQR
Sbjct: 97  ILEPGNPPKTDKAAILVDAVRMVTQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQR 156

Query: 61  LKADKEKLEQQVKAMSAPS-GFLPHPSSMSAAFA-AQSQVASNKLVPFIGYPGVAMWQFM 118
           LK +KEKLEQQ+KAM+AP   F P P  M  AFA AQ Q   NK+VP I YPGVAMWQFM
Sbjct: 157 LKTEKEKLEQQLKAMNAPQPSFFPAPPMMPTAFASAQGQAPGNKMVPIISYPGVAMWQFM 216

Query: 119 PPAAVDTSQDHVLRPPVA 136
           PPA+VDTSQDHVLRPPVA
Sbjct: 217 PPASVDTSQDHVLRPPVA 234

Transcription factor. Plays a role in resistance to amide-linked indole-3-acetic acid (IAA) conjugates such as IAA-Leu and IAA-Phe. May regulates gene expression in response to metal homeostasis changes.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  174 bits (440), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 89/140 (63%), Positives = 107/140 (76%), Gaps = 9/140 (6%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGR PKTDK  I++D +RM+ Q R EAQKLK     LQEKIKELK EKNELRDEKQ+
Sbjct: 92  VLEPGRTPKTDKVAIINDAIRMVNQARDEAQKLKDLNSSLQEKIKELKDEKNELRDEKQK 151

Query: 61  LKADKEKLEQQVKAM-SAPS---GFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQ 116
           LK +KE+++QQ+KA+ + P     FLP+P ++S     Q+Q   +KLVPF  YPG AMWQ
Sbjct: 152 LKVEKERIDQQLKAIKTQPQPQPCFLPNPQTLS-----QAQAPGSKLVPFTTYPGFAMWQ 206

Query: 117 FMPPAAVDTSQDHVLRPPVA 136
           FMPPAAVDTSQDHVLRPPVA
Sbjct: 207 FMPPAAVDTSQDHVLRPPVA 226

Arabidopsis thaliana (taxid: 3702)

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

 Score =  137 bits (344), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 74/137 (54%), Positives = 95/137 (69%), Gaps = 10/137 (7%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGR PKTDK  IL D +R++ QLR EA KL+++ + L E+IK LKAEKNELR+EK  
Sbjct: 156 VLEPGRTPKTDKPAILDDAIRILNQLRDEALKLEETNQKLLEEIKSLKAEKNELREEKLV 215

Query: 61  LKADKEKLEQQVKAMSAP-SGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMP 119
           LKADKEK EQQ+K+M+AP SGF+PH   + AAF        NK+  +  Y  + MW +MP
Sbjct: 216 LKADKEKTEQQLKSMTAPSSGFIPH---IPAAF------NHNKMAVYPSYGYMPMWHYMP 266

Query: 120 PAAVDTSQDHVLRPPVA 136
            +  DTS+D  LRPP A
Sbjct: 267 QSVRDTSRDQELRPPAA 283

Arabidopsis thaliana (taxid: 3702)

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

 Score =  122 bits (305), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 71/140 (50%), Positives = 95/140 (67%), Gaps = 11/140 (7%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGR PKTDK+ IL D +R++ QLR EA +L+++ + L E+IK LKA+KNELR+EK  
Sbjct: 188 VLEPGRTPKTDKSAILDDAIRVVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLV 247

Query: 61  LKADKEKLEQQVKAMSAPS-GFLP--HPSSMSAAFAAQSQVASNKLVPFIGY-PGVAMWQ 116
           LKA+KEK+EQQ+K+M  PS GF+P  HP    AAF +     +    P+  Y P + MW 
Sbjct: 248 LKAEKEKMEQQLKSMVVPSPGFMPSQHP----AAFHSHKMAVA---YPYGYYPPNMPMWS 300

Query: 117 FMPPAAVDTSQDHVLRPPVA 136
            +PPA  DTS+D    PPVA
Sbjct: 301 PLPPADRDTSRDLKNLPPVA 320

Arabidopsis thaliana (taxid: 3702)

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

 Score = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 37/88 (42%), Positives = 58/88 (65%), Gaps = 5/88 (5%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +L+P RP K DKATIL+D V+++++L +E  KLK     L ++ +EL  EKN+LR+EK  
Sbjct: 84  VLDPERP-KNDKATILTDTVQLLKELTSEVNKLKSEYTALTDESRELTQEKNDLREEKTS 142

Query: 61  LKADKEKL----EQQVKAMSAPSGFLPH 84
           LK+D E L    +Q++++MS     + H
Sbjct: 143 LKSDIENLNLQYQQRLRSMSPWGAAMDH 170

Arabidopsis thaliana (taxid: 3702)

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

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 41/109 (37%), Positives = 66/109 (60%), Gaps = 10/109 (9%)

Query: 2   LEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL 61
           L+P RP K+DKA++L+D ++M++ +  +  +LK   E L ++ +EL  EK+ELR+EK  L
Sbjct: 71  LDPNRP-KSDKASVLTDTIQMLKDVMNQVDRLKAEYETLSQESRELIQEKSELREEKATL 129

Query: 62  KADKEKLEQQ----VKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPF 106
           K+D E L  Q    +K M  P  ++PH  S    F A +Q  S+  +P+
Sbjct: 130 KSDIEILNAQYQHRIKTM-VP--WVPH-YSYHIPFVAITQGQSS-FIPY 173

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	136
297739325	223	unnamed protein product [Vitis vinifera]	1.0	0.609	0.838	2e-59
359485584	240	PREDICTED: transcription factor ILR3-lik	1.0	0.566	0.838	2e-59
297741862	225	unnamed protein product [Vitis vinifera]	1.0	0.604	0.764	4e-56
147785376	384	hypothetical protein VITISV_005283 [Viti	0.948	0.335	0.829	1e-55
359497014	232	PREDICTED: transcription factor ILR3-lik	1.0	0.586	0.764	2e-55
357474833	261	Transcription factor ILR3 [Medicago trun	1.0	0.521	0.779	1e-54
357474831	237	Transcription factor ILR3 [Medicago trun	1.0	0.573	0.779	1e-54
357452673	230	Transcription factor ILR3 [Medicago trun	1.0	0.591	0.779	9e-54
224114243	243	predicted protein [Populus trichocarpa]	1.0	0.559	0.705	3e-51
302398597	229	BHLH domain class transcription factor [	1.0	0.593	0.786	8e-51

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

 Score =  233 bits (594), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 114/136 (83%), Positives = 123/136 (90%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGRPPKTDKA ILSD VRM+ QLR+EAQKLK+S  DLQEKIKELKAEKNELRDEKQR
Sbjct: 88  ILEPGRPPKTDKAAILSDAVRMVTQLRSEAQKLKESNGDLQEKIKELKAEKNELRDEKQR 147

Query: 61  LKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPP 120
           LKA+KEKLEQQVKA+SA  GFLPHPS+M AAFAAQ +   NKL+PFIGYP VAMWQFMPP
Sbjct: 148 LKAEKEKLEQQVKAISAQPGFLPHPSAMPAAFAAQGRAPGNKLMPFIGYPSVAMWQFMPP 207

Query: 121 AAVDTSQDHVLRPPVA 136
           AAVDTSQDHVLRPPVA
Sbjct: 208 AAVDTSQDHVLRPPVA 223

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 =  233 bits (593), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 114/136 (83%), Positives = 123/136 (90%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGRPPKTDKA ILSD VRM+ QLR+EAQKLK+S  DLQEKIKELKAEKNELRDEKQR
Sbjct: 105 ILEPGRPPKTDKAAILSDAVRMVTQLRSEAQKLKESNGDLQEKIKELKAEKNELRDEKQR 164

Query: 61  LKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPP 120
           LKA+KEKLEQQVKA+SA  GFLPHPS+M AAFAAQ +   NKL+PFIGYP VAMWQFMPP
Sbjct: 165 LKAEKEKLEQQVKAISAQPGFLPHPSAMPAAFAAQGRAPGNKLMPFIGYPSVAMWQFMPP 224

Query: 121 AAVDTSQDHVLRPPVA 136
           AAVDTSQDHVLRPPVA
Sbjct: 225 AAVDTSQDHVLRPPVA 240

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  222 bits (565), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 104/136 (76%), Positives = 119/136 (87%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGRPPK DKA ILSD +RMM QLR+E QKLK+S EDLQEKI ELKAEKNELRDEKQR
Sbjct: 90  ILEPGRPPKMDKAVILSDALRMMTQLRSEGQKLKKSCEDLQEKINELKAEKNELRDEKQR 149

Query: 61  LKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPP 120
           LK +KE + QQ+KA+S+ +GFLPHPS++ A FAA  QV  +KL+PFIGYPGV+MWQFMPP
Sbjct: 150 LKTEKENIVQQIKALSSQAGFLPHPSAIPAPFAAPGQVVGSKLMPFIGYPGVSMWQFMPP 209

Query: 121 AAVDTSQDHVLRPPVA 136
           AAVDTSQDHVLRPPVA
Sbjct: 210 AAVDTSQDHVLRPPVA 225

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147785376|emb|CAN70830.1| hypothetical protein VITISV_005283 [Vitis vinifera]

 Score =  220 bits (560), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 107/129 (82%), Positives = 116/129 (89%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGRPPKTDKA ILSD VRM+ QLR+EAQKLK+S  DLQEKIKELKAEKNELRDEKQR
Sbjct: 79  ILEPGRPPKTDKAAILSDAVRMVTQLRSEAQKLKESNGDLQEKIKELKAEKNELRDEKQR 138

Query: 61  LKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPP 120
           LKA+KEKLEQQVKA+SA  GFLPHPS+M AAFAAQ +   NKL+PFIGYP VAMWQFMPP
Sbjct: 139 LKAEKEKLEQQVKAISAQPGFLPHPSAMPAAFAAQGRAPGNKLMPFIGYPSVAMWQFMPP 198

Query: 121 AAVDTSQDH 129
           AAVDTSQDH
Sbjct: 199 AAVDTSQDH 207

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  219 bits (559), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 104/136 (76%), Positives = 119/136 (87%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGRPPK DKA ILSD +RMM QLR+E QKLK+S EDLQEKI ELKAEKNELRDEKQR
Sbjct: 97  ILEPGRPPKMDKAVILSDALRMMTQLRSEGQKLKKSCEDLQEKINELKAEKNELRDEKQR 156

Query: 61  LKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPP 120
           LK +KE + QQ+KA+S+ +GFLPHPS++ A FAA  QV  +KL+PFIGYPGV+MWQFMPP
Sbjct: 157 LKTEKENIVQQIKALSSQAGFLPHPSAIPAPFAAPGQVVGSKLMPFIGYPGVSMWQFMPP 216

Query: 121 AAVDTSQDHVLRPPVA 136
           AAVDTSQDHVLRPPVA
Sbjct: 217 AAVDTSQDHVLRPPVA 232

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  217 bits (552), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 106/136 (77%), Positives = 116/136 (85%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGRP KTDKA IL D VRM+ QLR EAQKLK +   LQEKIKELK EKNELRDEKQR
Sbjct: 126 ILEPGRPAKTDKAAILIDAVRMVTQLRGEAQKLKDANSGLQEKIKELKVEKNELRDEKQR 185

Query: 61  LKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPP 120
           LKA+KEKLEQQ+K+M+AP  FLP P+++ AAFAAQ Q   NKLVPFI YPGVAMWQFMPP
Sbjct: 186 LKAEKEKLEQQLKSMNAPPSFLPTPTALPAAFAAQGQAHGNKLVPFISYPGVAMWQFMPP 245

Query: 121 AAVDTSQDHVLRPPVA 136
           AAVDTSQDHVLRPPVA
Sbjct: 246 AAVDTSQDHVLRPPVA 261

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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 =  217 bits (552), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 106/136 (77%), Positives = 116/136 (85%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGRP KTDKA IL D VRM+ QLR EAQKLK +   LQEKIKELK EKNELRDEKQR
Sbjct: 102 ILEPGRPAKTDKAAILIDAVRMVTQLRGEAQKLKDANSGLQEKIKELKVEKNELRDEKQR 161

Query: 61  LKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPP 120
           LKA+KEKLEQQ+K+M+AP  FLP P+++ AAFAAQ Q   NKLVPFI YPGVAMWQFMPP
Sbjct: 162 LKAEKEKLEQQLKSMNAPPSFLPTPTALPAAFAAQGQAHGNKLVPFISYPGVAMWQFMPP 221

Query: 121 AAVDTSQDHVLRPPVA 136
           AAVDTSQDHVLRPPVA
Sbjct: 222 AAVDTSQDHVLRPPVA 237

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  214 bits (545), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 106/136 (77%), Positives = 115/136 (84%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGRPPKTDKA IL D VRM+ QLR EAQKLK S   LQEKIKELK EKNELRDEKQR
Sbjct: 95  ILEPGRPPKTDKAAILIDAVRMVTQLRGEAQKLKDSNSGLQEKIKELKVEKNELRDEKQR 154

Query: 61  LKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPP 120
           LKA+KEKLEQQVK+M+   GFL HP ++ AAFA Q Q  SNKL+PF+ YPGVAMWQFMPP
Sbjct: 155 LKAEKEKLEQQVKSMNTQPGFLTHPPAIPAAFAHQGQAPSNKLMPFMSYPGVAMWQFMPP 214

Query: 121 AAVDTSQDHVLRPPVA 136
           AAVDTSQDHVLRPPVA
Sbjct: 215 AAVDTSQDHVLRPPVA 230

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  206 bits (523), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 96/136 (70%), Positives = 113/136 (83%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +L+PGRPPK DK+ IL D  RM+ QLR E+QKLK+S   LQEKI ELKAEKNELRDEKQR
Sbjct: 108 LLDPGRPPKVDKSAILVDAARMVTQLRDESQKLKESNVSLQEKIDELKAEKNELRDEKQR 167

Query: 61  LKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPP 120
           LK +KE LE+QVKA+S P  FLPHPS++ A F+A  QV  +KL+PF+GYPG++MWQFMPP
Sbjct: 168 LKTEKENLERQVKALSTPPNFLPHPSAIPAPFSAPGQVVGSKLMPFVGYPGISMWQFMPP 227

Query: 121 AAVDTSQDHVLRPPVA 136
           A VDTSQDHVLRPPVA
Sbjct: 228 AVVDTSQDHVLRPPVA 243

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  204 bits (520), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 107/136 (78%), Positives = 118/136 (86%)

Query: 1   MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
           +LEPGRPPKTDKA IL D VRM+ QLR EAQKLK +   LQEKIKELKAEKNELRDEKQR
Sbjct: 94  ILEPGRPPKTDKAAILVDAVRMVNQLRGEAQKLKDTNSGLQEKIKELKAEKNELRDEKQR 153

Query: 61  LKADKEKLEQQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPP 120
           LK++KEKLEQQ+K+M+   GFLP P ++ AAFAAQSQ   NK+VPFIGYPGVAMWQFMPP
Sbjct: 154 LKSEKEKLEQQLKSMNVQPGFLPPPPAIPAAFAAQSQARGNKMVPFIGYPGVAMWQFMPP 213

Query: 121 AAVDTSQDHVLRPPVA 136
           AAVDTSQDHVLRPPVA
Sbjct: 214 AAVDTSQDHVLRPPVA 229

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

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	136
TAIR|locus:2157538	234	ILR3 "AT5G54680" [Arabidopsis	1.0	0.581	0.688	1.9e-44
UNIPROTKB|Q6ZKI8	253	OJ1119_D01.9 "BHLH transcripti	0.992	0.533	0.537	1.3e-34
TAIR|locus:2129710	283	bHLH104 "AT4G14410" [Arabidops	0.933	0.448	0.518	3.8e-30
UNIPROTKB|Q6ZGM4	236	OJ1442_E05.19 "cDNA clone:006-	1.0	0.576	0.517	4.9e-30
TAIR|locus:2086198	320	bHLH34 "AT3G23210" [Arabidopsi	0.941	0.4	0.489	7.3e-27
TAIR|locus:2092216	337	bHLH121 "AT3G19860" [Arabidops	0.610	0.246	0.420	8.2e-12
UNIPROTKB|Q67U21	343	OSJNBa0065F08.2 "Basic helix-l	0.507	0.201	0.485	2.4e-11
TAIR|locus:2135169	286	bHLH11 "AT4G36060" [Arabidopsi	0.602	0.286	0.380	2.3e-10
UNIPROTKB|Q60EM5	77	OJ1651_D06.8 "Putative unchara	0.448	0.792	0.358	7e-06
UNIPROTKB|Q69V10	265	P0506F02.119 "cDNA clone:J0230	0.529	0.271	0.246	7.9e-06

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

 Score = 468 (169.8 bits), Expect = 1.9e-44, P = 1.9e-44
 Identities = 95/138 (68%), Positives = 103/138 (74%)

Query:     1 MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
             +LEPG PPKTDKA IL D VRM+ QLR EAQKLK S   LQ+KIKELK EKNELRDEKQR
Sbjct:    97 ILEPGNPPKTDKAAILVDAVRMVTQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQR 156

Query:    61 LKADKEKLEQQVKAMSAPS-GFLPHPXXXXXXXXXXXXXX-XNKLVPFIGYPGVAMWQFM 118
             LK +KEKLEQQ+KAM+AP   F P P                NK+VP I YPGVAMWQFM
Sbjct:   157 LKTEKEKLEQQLKAMNAPQPSFFPAPPMMPTAFASAQGQAPGNKMVPIISYPGVAMWQFM 216

Query:   119 PPAAVDTSQDHVLRPPVA 136
             PPA+VDTSQDHVLRPPVA
Sbjct:   217 PPASVDTSQDHVLRPPVA 234

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 375 (137.1 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 78/145 (53%), Positives = 97/145 (66%)

Query:     2 LEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL 61
             LEPG+P K+DKA ILSD  RM+ QLR EA++LK + E L++KIKELKAEK+ELRDEKQ+L
Sbjct:   109 LEPGKPVKSDKAAILSDATRMVIQLRAEAKQLKDTNESLEDKIKELKAEKDELRDEKQKL 168

Query:    62 KADKEKLEQQVKAMSAPSGFLPHPXXXXX---------XXXXXXXXXXNKLV-PFIGYPG 111
             K +KE LEQQVK ++A   ++PHP                         KL+ PF+GYPG
Sbjct:   169 KVEKETLEQQVKILTATPAYMPHPTLMPAPYPQAPLAPFHHAQGQAAGQKLMMPFVGYPG 228

Query:   112 VAMWQFMPPAAVDTSQDHVLRPPVA 136
               MWQFMPP+ VDTS+D    PPVA
Sbjct:   229 YPMWQFMPPSEVDTSKDSEACPPVA 253

GO:0005634 "nucleus" evidence=IC

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

 Score = 333 (122.3 bits), Expect = 3.8e-30, P = 3.8e-30
 Identities = 71/137 (51%), Positives = 91/137 (66%)

Query:     1 MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
             +LEPGR PKTDK  IL D +R++ QLR EA KL+++ + L E+IK LKAEKNELR+EK  
Sbjct:   156 VLEPGRTPKTDKPAILDDAIRILNQLRDEALKLEETNQKLLEEIKSLKAEKNELREEKLV 215

Query:    61 LKADKEKLEQQVKAMSAPS-GFLPHPXXXXXXXXXXXXXXXNKLVPFIGYPGVAMWQFMP 119
             LKADKEK EQQ+K+M+APS GF+PH                NK+  +  Y  + MW +MP
Sbjct:   216 LKADKEKTEQQLKSMTAPSSGFIPH---------IPAAFNHNKMAVYPSYGYMPMWHYMP 266

Query:   120 PAAVDTSQDHVLRPPVA 136
              +  DTS+D  LRPP A
Sbjct:   267 QSVRDTSRDQELRPPAA 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|Q6ZGM4 OJ1442_E05.19 "cDNA clone:006-303-B03, full insert sequence" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 75/145 (51%), Positives = 94/145 (64%)

Query:     1 MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
             ++ P +  K DKA ILSD  R++ +LR EA+KLK+S E L+E IK+LK EKNELRDEK  
Sbjct:    92 VINPDKQAKLDKANILSDAARLLAELRGEAEKLKESNEKLRETIKDLKVEKNELRDEKVT 151

Query:    61 LKADKEKLEQQVKAMS-APSGF---LPHPXXXXXXXXXXXX----XXXNKLVPF-IGYPG 111
             LKA+KE+LEQQVKA+S AP+GF   LPHP                   NK  P    + G
Sbjct:   152 LKAEKERLEQQVKALSVAPTGFVPHLPHPAAFHPAAFPPFIPPYQALGNKNAPTPAAFQG 211

Query:   112 VAMWQFMPPAAVDTSQDHVLRPPVA 136
             +AMWQ++PP AVDT+QD  L PP A
Sbjct:   212 MAMWQWLPPTAVDTTQDPKLWPPNA 236

GO:0005634 "nucleus" evidence=IC

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

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 69/141 (48%), Positives = 91/141 (64%)

Query:     1 MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
             +LEPGR PKTDK+ IL D +R++ QLR EA +L+++ + L E+IK LKA+KNELR+EK  
Sbjct:   188 VLEPGRTPKTDKSAILDDAIRVVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLV 247

Query:    61 LKADKEKLEQQVKAMSAPS-GFLP--HPXXXXXXXXXXXXXXXNKLVPFIGY--PGVAMW 115
             LKA+KEK+EQQ+K+M  PS GF+P  HP                   P+ GY  P + MW
Sbjct:   248 LKAEKEKMEQQLKSMVVPSPGFMPSQHPAAFHSHKMAVAY-------PY-GYYPPNMPMW 299

Query:   116 QFMPPAAVDTSQDHVLRPPVA 136
               +PPA  DTS+D    PPVA
Sbjct:   300 SPLPPADRDTSRDLKNLPPVA 320

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

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

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

 Score = 165 (63.1 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 37/88 (42%), Positives = 58/88 (65%)

Query:     1 MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
             +L+P RP K DKATIL+D V+++++L +E  KLK     L ++ +EL  EKN+LR+EK  
Sbjct:    84 VLDPERP-KNDKATILTDTVQLLKELTSEVNKLKSEYTALTDESRELTQEKNDLREEKTS 142

Query:    61 LKADKEKL----EQQVKAMSAPSGFLPH 84
             LK+D E L    +Q++++MS     + H
Sbjct:   143 LKSDIENLNLQYQQRLRSMSPWGAAMDH 170

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

 Score = 161 (61.7 bits), Expect = 2.4e-11, P = 2.4e-11
 Identities = 34/70 (48%), Positives = 46/70 (65%)

Query:     2 LEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL 61
             L+P RP + DKATILSD ++M++ L ++  KLK     L E+ +EL  EKNELRDEK  L
Sbjct:    66 LDPDRP-RNDKATILSDAIQMLKDLTSQVNKLKAEYTSLSEEARELTQEKNELRDEKVSL 124

Query:    62 KADKEKLEQQ 71
             K + + L  Q
Sbjct:   125 KFEVDNLNTQ 134

GO:0005634 "nucleus" evidence=IC

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

 Score = 150 (57.9 bits), Expect = 2.3e-10, P = 2.3e-10
 Identities = 32/84 (38%), Positives = 54/84 (64%)

Query:     2 LEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL 61
             L+P RP K+DKA++L+D ++M++ +  +  +LK   E L ++ +EL  EK+ELR+EK  L
Sbjct:    71 LDPNRP-KSDKASVLTDTIQMLKDVMNQVDRLKAEYETLSQESRELIQEKSELREEKATL 129

Query:    62 KADKEKLEQQVK-AMSAPSGFLPH 84
             K+D E L  Q +  +     ++PH
Sbjct:   130 KSDIEILNAQYQHRIKTMVPWVPH 153

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|Q60EM5 OJ1651_D06.8 "Putative uncharacterized protein OJ1651_D06.8" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 104 (41.7 bits), Expect = 7.0e-06, P = 7.0e-06
 Identities = 24/67 (35%), Positives = 34/67 (50%)

Query:    76 SAPSGFLPHPXXXXXXXXX----XXXXXXNKLVPFI-GY-PGVAMWQFMPPAAVDTSQDH 129
             +AP+ F+PH                     K VP+   Y P  A WQ++PP ++DTS+D 
Sbjct:    11 AAPAPFVPHHAAAVAAAPAYHPAAFAQAGGKYVPYATSYAPPAAFWQWIPPTSLDTSKDP 70

Query:   130 VLRPPVA 136
             V+ PPVA
Sbjct:    71 VMWPPVA 77

GO:0005634 "nucleus" evidence=IC

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

 Score = 94 (38.1 bits), Expect = 7.9e-06, Sum P(2) = 7.9e-06
 Identities = 18/73 (24%), Positives = 41/73 (56%)

Query:     1 MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQR 60
             +LEP R     KA +L +  R+++ L ++ + L++    L+ +   +  E+NEL D+   
Sbjct:    61 LLEPDRQ-NNGKACVLGETTRILKDLLSQVESLRKENSSLKNESHYVALERNELHDDNSM 119

Query:    61 LKADKEKLEQQVK 73
             L+ +  +L+ +++
Sbjct:   120 LRTEILELQNELR 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	0.7391	1.0	0.5811	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	136
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-05
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	5e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-05
pfam04111	356	pfam04111, APG6, Autophagy protein Apg6	8e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-04
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	2e-04
pfam04977	80	pfam04977, DivIC, Septum formation initiator	2e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	3e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	3e-04
COG4026	290	COG4026, COG4026, Uncharacterized protein containi	3e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	3e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	4e-04
PRK05771	646	PRK05771, PRK05771, V-type ATP synthase subunit I;	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-04
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	7e-04
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	0.001
COG4026	290	COG4026, COG4026, Uncharacterized protein containi	0.001
smart00338	65	smart00338, BRLZ, basic region leucin zipper	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.002
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.002
PRK13729	475	PRK13729, PRK13729, conjugal transfer pilus assemb	0.002
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	0.002
pfam10211	189	pfam10211, Ax_dynein_light, Axonemal dynein light	0.002
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.003
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.003
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	0.003
pfam08317	321	pfam08317, Spc7, Spc7 kinetochore protein	0.003
pfam13870	177	pfam13870, DUF4201, Domain of unknown function (DU	0.003
pfam09798	648	pfam09798, LCD1, DNA damage checkpoint protein	0.003
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	0.004
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.004
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.004
TIGR03545	555	TIGR03545, TIGR03545, TIGR03545 family protein	0.004
pfam12329	74	pfam12329, TMF_DNA_bd, TATA element modulatory fac	0.004
pfam01025	165	pfam01025, GrpE, GrpE	0.004
TIGR02894	161	TIGR02894, DNA_bind_RsfA, transcription factor, Rs	0.004
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.004

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

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 19/59 (32%), Positives = 39/59 (66%)

Query: 16  LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 74
           L ++ R +E+L+ E   L++  E LQ +++EL+ E  EL +E + L+   E+LE+++++
Sbjct: 711 LEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELES 769

Length = 1163

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

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 16/49 (32%), Positives = 33/49 (67%)

Query: 23  MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ 71
           + +L+ E  +L++   +LQE++ EL+ E  EL+ E   L+A+ E+L+++
Sbjct: 68  LPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKE 116

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

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

 Score = 40.9 bits (96), Expect = 6e-05
 Identities = 17/68 (25%), Positives = 37/68 (54%)

Query: 10  TDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE 69
              + +L ++  + E LR E  +L+    +++ +++ELK E   L +  +RL    E L+
Sbjct: 365 EKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLK 424

Query: 70  QQVKAMSA 77
           +++K + A
Sbjct: 425 EELKELEA 432

Length = 1163

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

 Score = 40.6 bits (95), Expect = 8e-05
 Identities = 17/48 (35%), Positives = 31/48 (64%)

Query: 24  EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ 71
           E L +E  +LK+  E L ++++EL+ E ++L  E   L+ +KE+LE +
Sbjct: 66  EALDSELDELKKEEERLLDELEELEKEDDDLDGELVELQEEKEQLENE 113

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

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

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 18/67 (26%), Positives = 40/67 (59%)

Query: 11  DKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ 70
           +    L D+   +E++  E  + +   +D +EK+++LK E NEL+ E  RL+ + ++L +
Sbjct: 361 ELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSE 420

Query: 71  QVKAMSA 77
           ++  ++A
Sbjct: 421 ELADLNA 427

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

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

 Score = 39.4 bits (93), Expect = 2e-04
 Identities = 16/48 (33%), Positives = 30/48 (62%)

Query: 23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ 70
          +E L     +L++    L+ K+++L+AE  +L  E +RLK++ EKL+ 
Sbjct: 3  LEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKS 50

Length = 389

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

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 15/43 (34%), Positives = 26/43 (60%)

Query: 31 QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 73
           +L Q    LQ ++ +LKAE  EL  E + LK+D + +E++ +
Sbjct: 20 YQLNQEIAALQAELAKLKAENEELEAEVKDLKSDPDYIEERAR 62

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

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 15/59 (25%), Positives = 35/59 (59%)

Query: 15  ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 73
            L ++ + + +L  E + L++  ++LQE+  +LK +   +  E + L   KE+LE++++
Sbjct: 813 RLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELE 871

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

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

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 7/69 (10%)

Query: 16  LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEK-------NELRDEKQRLKADKEKL 68
           L +V++ +++     +K  + TE+++E IKE + E        NE+  E   L+ + EKL
Sbjct: 167 LGEVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKL 226

Query: 69  EQQVKAMSA 77
           E++VK +  
Sbjct: 227 EKEVKELEE 235

Length = 880

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

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 16/58 (27%), Positives = 39/58 (67%)

Query: 16  LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 73
             D+    E+L+ + ++L++  E+L ++++EL+AE  E+++  +RL+ +  +LE+ +K
Sbjct: 130 YMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLK 187

Length = 290

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 21/66 (31%), Positives = 37/66 (56%)

Query: 16  LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 75
             +V+   E+ R E + L+   EDL+E I E + E+ EL +E + L+   E+LE++   +
Sbjct: 239 ADEVLEEHEERREELETLEAEIEDLRETIAETEREREELAEEVRDLRERLEELEEERDDL 298

Query: 76  SAPSGF 81
            A +G 
Sbjct: 299 LAEAGL 304

Length = 880

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 19/54 (35%), Positives = 34/54 (62%)

Query: 23  MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS 76
            E+L  E ++L++  E+L+EK+ EL+ E  EL  E + LK + E+LE + + + 
Sbjct: 823 RERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELE 876

Length = 1163

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 18/56 (32%), Positives = 35/56 (62%)

Query: 16  LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ 71
           + ++ + +EQL  E +KLK+  E+L+E +  L+ E   ++ E + L+A  E+LE+ 
Sbjct: 718 IGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEED 773

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

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

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 11  DKATILSDVVRMMEQLRTE--AQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL 68
            K   L +  + +     E   + +++  E ++++IKEL+ E +EL +E + L+ + E+L
Sbjct: 67  PKLNPLREEKKKVSVKSLEELIKDVEEELEKIEKEIKELEEEISELENEIKELEQEIERL 126

Query: 69  E 69
           E
Sbjct: 127 E 127

Length = 646

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

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 18/59 (30%), Positives = 40/59 (67%)

Query: 16  LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 74
           L  + R +E L    ++L+Q  E+L+E+I+EL+ + +EL +E + L+ + E+L+++++ 
Sbjct: 809 LDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEE 867

Length = 1163

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

 Score = 37.9 bits (89), Expect = 7e-04
 Identities = 11/54 (20%), Positives = 34/54 (62%)

Query: 29 EAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFL 82
            + L++   +L+E+I++L+ +  +L  E ++L+ + E+L+ +++ + +P   +
Sbjct: 2  RLEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSPPLIV 55

Length = 389

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 16/52 (30%), Positives = 29/52 (55%)

Query: 26  LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA 77
            R    +L+Q   +LQE++ EL+ +  EL+ E Q LK +   LE +++ +  
Sbjct: 64  ARERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQK 115

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

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

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 18/47 (38%), Positives = 34/47 (72%)

Query: 29  EAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 75
           E   LK+  E+L+EK++EL+ EK EL  E + L+A+ E++++++K +
Sbjct: 129 EYMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRL 175

Length = 290

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

 Score = 34.8 bits (81), Expect = 0.001
 Identities = 14/44 (31%), Positives = 30/44 (68%)

Query: 31 QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 74
          ++ K   E+L+ K+++L+AE   L+ E +RL+ + EKL+ +++ 
Sbjct: 22 ERKKAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSELEE 65

Length = 65

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 15/65 (23%), Positives = 36/65 (55%)

Query: 11   DKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ 70
             + T+ +++ R +E+L  E + L        E+ +E++    EL+ +++ L+  KEKL +
Sbjct: 939  YEDTLETELEREIERLEEEIEALGPVNLRAIEEYEEVEERYEELKSQREDLEEAKEKLLE 998

Query: 71   QVKAM 75
             ++ +
Sbjct: 999  VIEEL 1003

Length = 1163

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 15/53 (28%), Positives = 29/53 (54%)

Query: 24  EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS 76
           EQL     +L +   +L+ +I+EL+    E  +E    +A+ E+LE Q++ + 
Sbjct: 743 EQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLK 795

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

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 17/60 (28%), Positives = 42/60 (70%)

Query: 16  LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 75
           L+++ R +E+L  + ++L+   ++L E++ EL+ +  EL++E + L+A+ E+LE +++ +
Sbjct: 311 LANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEEL 370

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

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 28/125 (22%), Positives = 46/125 (36%), Gaps = 16/125 (12%)

Query: 10  TDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE 69
           T+     + + +  E++R E   L +   D Q +I++L  +   L ++   +KA      
Sbjct: 72  TEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQ---VKALGANPV 128

Query: 70  ----QQVKAMSAPSGFL---PHPSSMSAAFAAQSQVASNKLVPFIGYPGVAMWQFMPPAA 122
               + V  M A        P P +   +F  Q  VA      F  YPG      + P  
Sbjct: 129 TATGEPVPQMPASPPGPEGEPQPGNTPVSFPPQGSVAVPPPTAF--YPGNG----VTPPP 182

Query: 123 VDTSQ 127
             T Q
Sbjct: 183 QVTYQ 187

Length = 475

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

 Score = 36.7 bits (86), Expect = 0.002
 Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 6/54 (11%)

Query: 21  RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 74
           R +EQ   EA+ L +  E L+E   EL+ +K +L++E+ +L    E+ E++ + 
Sbjct: 530 RELEQKAEEAEALLKEAEKLKE---ELEEKKEKLQEEEDKL---LEEAEKEAQQ 577

Length = 782

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 16/68 (23%), Positives = 37/68 (54%), Gaps = 15/68 (22%)

Query: 23  MEQLRTEAQKLKQSTEDLQEKIKELKAEKNEL--RDEKQR-------------LKADKEK 67
             +L  E +KL++  E+L++++ EL+A+   +  R+E++R             LK   ++
Sbjct: 122 KSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREEEERQIEEKRHADEIAFLKKQNQQ 181

Query: 68  LEQQVKAM 75
           L+ Q++ +
Sbjct: 182 LKSQLEQI 189

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

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 14/48 (29%), Positives = 29/48 (60%)

Query: 24  EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ 71
           E+L+ E ++L Q  E L  + ++L   +N+L + ++ L A + +LE+ 
Sbjct: 77  EELQREEERLVQKEEQLDARAEKLDNLENQLEEREKALSARELELEEL 124

Length = 508

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

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 15/62 (24%), Positives = 35/62 (56%)

Query: 16  LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 75
           + ++   +  LR   ++L+   E+L+E+++ELK +   L++E +  +   E+LEQ +  +
Sbjct: 297 IEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAEL 356

Query: 76  SA 77
             
Sbjct: 357 EE 358

Length = 1163

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

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 19/59 (32%), Positives = 34/59 (57%)

Query: 15  ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 73
            L +    +E+L  E Q+L++  E+L+ ++ EL+ E  EL+ E   L  +  +LEQQ +
Sbjct: 247 ELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQ 305

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

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 18/54 (33%), Positives = 33/54 (61%)

Query: 24  EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA 77
           E+LR E  +L++  E+LQ+++  L  E + L  +KQ L+     LE+Q++ + A
Sbjct: 270 EELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEA 323

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

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 2/55 (3%)

Query: 22  MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKA--DKEKLEQQVKA 74
           ++  L    ++L+Q  E+ +  +KE +  K EL ++K++L+   DK   E + +A
Sbjct: 521 LIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEA 575

Length = 782

>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 16  LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRD--EKQRLKADKE--KLEQQ 71
           +S+  + +E+L+ E Q+L  + E L  K  EL  E  E     E+ R  + KE  KL+ +
Sbjct: 223 ISEKRKQLEELQQELQELTIAIEALTNKKSELLEEIAEAEKIREECRGWSAKEISKLKAK 282

Query: 72  VKAMSAPSGF 81
           V  +   +G+
Sbjct: 283 VSLLQKLTGW 292

This domain is found in cell division proteins which are required for kinetochore-spindle association. Length = 321

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 14/54 (25%), Positives = 33/54 (61%)

Query: 26  LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS 79
           L  E ++LK+  ++ +E++ +L+ E  +++ E+ +L+   +KL QQ   +  P+
Sbjct: 89  LEEELERLKKELKEKEERLAKLRKELYKVKLERDKLRKQNKKLRQQGGLLHVPA 142

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

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

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 7/95 (7%)

Query: 15  ILSDVVRMME-QLRTEAQKLKQSTEDLQEK----IKELKAEKNELRDEKQRLKADKEKLE 69
           +L D + M++ Q + E  K K    +L+EK    +++LK E   L DE++ L  ++  L 
Sbjct: 1   MLRDKLDMLQQQKQEERNKQKSRVNELKEKHDQELQKLKQELQSLEDERKFLVLEQRGLS 60

Query: 70  --QQVKAMSAPSGFLPHPSSMSAAFAAQSQVASNK 102
                  +S PS  L    +   A  +Q      K
Sbjct: 61  ANDLRTELSPPSNLLKTSDASHIADESQPNSIKQK 95

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

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

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 15/58 (25%), Positives = 35/58 (60%)

Query: 13  ATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ 70
              L ++ + + +L+ E  +L++   +LQ++ +ELK E + L  E +RL+ +  +++Q
Sbjct: 65  RERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQ 122

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

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

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 14/52 (26%), Positives = 31/52 (59%)

Query: 24  EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 75
           + +  E + L    E+L+E+++EL+A   +L      LK ++++LE Q++ +
Sbjct: 850 KSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLREL 901

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

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

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 17/74 (22%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 14  TILSDVVRMMEQLRTEAQKLKQSTEDLQ---EKIKELKAEKNELRDEKQRLKADKEKLEQ 70
            I  ++ ++ ++     ++L++  EDL    ++I+ +K+E  EL    + L+ D  KLE+
Sbjct: 720 EIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEE 779

Query: 71  QV---KAMSAPSGF 81
            +   +A  + S  
Sbjct: 780 ALNDLEARLSHSRI 793

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|234252 TIGR03545, TIGR03545, TIGR03545 family protein

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 12/47 (25%), Positives = 27/47 (57%)

Query: 31  QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA 77
            +L++  E+  +  KE KA+K +++  K  L+ DK++L+  +  +  
Sbjct: 212 LELQKIKEEFDKLKKEGKADKQKIKSAKNDLQNDKKQLKADLAELKK 258

This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair. Length = 555

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

 Score = 33.8 bits (78), Expect = 0.004
 Identities = 18/51 (35%), Positives = 27/51 (52%)

Query: 22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV 72
           + QL  E +KL +        IK+L+A+  EL  E   LK   EKLE+++
Sbjct: 13 QIAQLMEEGEKLSKKELKHNNTIKKLRAKNKELEKEIAELKKKLEKLEKEL 63

This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. Length = 74

>gnl|CDD|216249 pfam01025, GrpE, GrpE

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 15/46 (32%), Positives = 28/46 (60%)

Query: 28 TEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 73
           E ++L+   E L+E+++EL+ E  EL+D   RL A+ E   ++ +
Sbjct: 4  EEEEELEDEEEALEEELEELEEEIEELKDRLLRLLAEFENYRKRTE 49

Length = 165

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

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 14/46 (30%), Positives = 26/46 (56%)

Query: 23  MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL 68
            + L+ E ++LK   E LQ++ +EL+ E  +LR     ++ D + L
Sbjct: 99  DQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTL 144

In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO [Regulatory functions, DNA interactions, Cellular processes, Sporulation and germination]. Length = 161

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

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 12/51 (23%), Positives = 30/51 (58%)

Query: 21  RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ 71
             ++    E ++L++  E+L+EKI+ L+  + E+ + ++ L+  +  LE+ 
Sbjct: 267 EALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEEL 317

Length = 908

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	136
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	97.59
PRK15422	79	septal ring assembly protein ZapB; Provisional	97.59
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	97.29
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	97.2
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	97.11
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	96.95
smart00353	53	HLH helix loop helix domain.	96.78
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	96.73
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	96.53
PRK15422	79	septal ring assembly protein ZapB; Provisional	96.45
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	96.28
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	96.25
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	96.18
smart00338	65	BRLZ basic region leucin zipper.	96.15
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	96.11
COG4026	290	Uncharacterized protein containing TOPRIM domain,	96.1
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	96.09
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	96.05
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	96.0
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	95.96
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	95.93
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	95.93
PRK10884	206	SH3 domain-containing protein; Provisional	95.91
PF04880	166	NUDE_C: NUDE protein, C-terminal conserved region;	95.79
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	95.63
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	95.61
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	95.53
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	95.48
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	95.4
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	95.35
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	95.26
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	95.21
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	95.18
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	95.17
COG4026	290	Uncharacterized protein containing TOPRIM domain,	95.15
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	95.15
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	95.1
PRK13169	110	DNA replication intiation control protein YabA; Re	95.04
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	95.03
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	94.98
PRK11637	428	AmiB activator; Provisional	94.92
PRK11637	428	AmiB activator; Provisional	94.79
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	94.7
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	94.63
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	94.63
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	94.63
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	94.56
KOG2391	365	consensus Vacuolar sorting protein/ubiquitin recep	94.56
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	94.55
PF04325	49	DUF465: Protein of unknown function (DUF465); Inte	94.53
PRK09039	343	hypothetical protein; Validated	94.52
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	94.48
PRK13922	276	rod shape-determining protein MreC; Provisional	94.45
PRK10884	206	SH3 domain-containing protein; Provisional	94.45
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	94.42
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	94.39
PF14662	193	CCDC155: Coiled-coil region of CCDC155	94.37
COG5570	57	Uncharacterized small protein [Function unknown]	94.37
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	94.26
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	94.25
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	94.23
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	94.19
PF15294	278	Leu_zip: Leucine zipper	94.11
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	94.01
PRK13169	110	DNA replication intiation control protein YabA; Re	93.99
PF07989	75	Microtub_assoc: Microtubule associated; InterPro:	93.93
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	93.9
PF14662	193	CCDC155: Coiled-coil region of CCDC155	93.86
smart00338	65	BRLZ basic region leucin zipper.	93.74
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	93.69
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	93.66
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	93.65
TIGR02209	85	ftsL_broad cell division protein FtsL. This model	93.63
PRK00888	105	ftsB cell division protein FtsB; Reviewed	93.62
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	93.6
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	93.42
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	93.35
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	93.35
PF00038	312	Filament: Intermediate filament protein; InterPro:	93.32
PHA02562	562	46 endonuclease subunit; Provisional	93.28
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	93.24
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	93.23
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	93.21
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	93.16
PRK05771	646	V-type ATP synthase subunit I; Validated	93.15
TIGR02209	85	ftsL_broad cell division protein FtsL. This model	93.06
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	93.04
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	93.02
PF14282	106	FlxA: FlxA-like protein	92.99
PRK13922	276	rod shape-determining protein MreC; Provisional	92.94
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	92.9
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	92.69
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	92.67
PF10186	302	Atg14: UV radiation resistance protein and autopha	92.59
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	92.58
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	92.55
PF13815	118	Dzip-like_N: Iguana/Dzip1-like DAZ-interacting pro	92.54
PRK05431	425	seryl-tRNA synthetase; Provisional	92.54
PHA03011	120	hypothetical protein; Provisional	92.45
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	92.34
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	92.33
PF00038	312	Filament: Intermediate filament protein; InterPro:	92.21
PRK03992	389	proteasome-activating nucleotidase; Provisional	92.2
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	92.18
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	92.16
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	92.16
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	92.15
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	92.1
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	91.99
TIGR01554	378	major_cap_HK97 phage major capsid protein, HK97 fa	91.89
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	91.86
KOG4360	596	consensus Uncharacterized coiled coil protein [Fun	91.83
PF10186	302	Atg14: UV radiation resistance protein and autopha	91.82
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	91.81
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	91.76
PRK09039	343	hypothetical protein; Validated	91.72
PF01920	106	Prefoldin_2: Prefoldin subunit; InterPro: IPR00277	91.7
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	91.66
KOG1318	411	consensus Helix loop helix transcription factor EB	91.58
PRK11415	74	hypothetical protein; Provisional	91.56
cd00632	105	Prefoldin_beta Prefoldin beta; Prefoldin is a hexa	91.54
PRK03992	389	proteasome-activating nucleotidase; Provisional	91.48
PRK00888	105	ftsB cell division protein FtsB; Reviewed	91.44
TIGR02231	525	conserved hypothetical protein. This family consis	91.35
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	91.34
KOG4797	123	consensus Transcriptional regulator [Transcription	91.25
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	91.23
PF05837	106	CENP-H: Centromere protein H (CENP-H); InterPro: I	91.15
TIGR00414	418	serS seryl-tRNA synthetase. This model represents	91.08
PF14282	106	FlxA: FlxA-like protein	90.94
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	90.94
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	90.93
KOG1962	216	consensus B-cell receptor-associated protein and r	90.92
PRK00409	782	recombination and DNA strand exchange inhibitor pr	90.75
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	90.75
COG4942	420	Membrane-bound metallopeptidase [Cell division and	90.7
COG2433	652	Uncharacterized conserved protein [Function unknow	90.65
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	90.6
PF01166	59	TSC22: TSC-22/dip/bun family; InterPro: IPR000580	90.58
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	90.52
PF14988	206	DUF4515: Domain of unknown function (DUF4515)	90.49
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	90.48
PF07334	76	IFP_35_N: Interferon-induced 35 kDa protein (IFP 3	90.41
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	90.41
COG2433	652	Uncharacterized conserved protein [Function unknow	90.39
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	90.38
PF05008	79	V-SNARE: Vesicle transport v-SNARE protein N-termi	90.36
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	90.28
PF03961	451	DUF342: Protein of unknown function (DUF342); Inte	90.13
PF14645	116	Chibby: Chibby family	89.99
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	89.96
PF10498	359	IFT57: Intra-flagellar transport protein 57 ; Inte	89.93
PLN02678	448	seryl-tRNA synthetase	89.93
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	89.88
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	89.58
PF05103	131	DivIVA: DivIVA protein; InterPro: IPR007793 The Ba	89.49
PF12709	87	Kinetocho_Slk19: Central kinetochore-associated; I	89.41
PF05701	522	WEMBL: Weak chloroplast movement under blue light;	89.39
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	89.38
PF04999	97	FtsL: Cell division protein FtsL; InterPro: IPR007	89.32
PRK04325	74	hypothetical protein; Provisional	89.32
COG3937	108	Uncharacterized conserved protein [Function unknow	89.31
PF03961	451	DUF342: Protein of unknown function (DUF342); Inte	89.3
PF12709	87	Kinetocho_Slk19: Central kinetochore-associated; I	89.19
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	89.14
PF10458	66	Val_tRNA-synt_C: Valyl tRNA synthetase tRNA bindin	89.11
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	89.1
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	89.1
COG2919	117	Septum formation initiator [Cell division and chro	89.04
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	88.96
COG5481	67	Uncharacterized conserved small protein containing	88.89
PRK02119	73	hypothetical protein; Provisional	88.84
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	88.79
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	88.56
PRK14153	194	heat shock protein GrpE; Provisional	88.53
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	88.53
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	88.4
PF08961	243	DUF1875: Domain of unknown function (DUF1875); Int	88.21
KOG2751	447	consensus Beclin-like protein [Signal transduction	88.19
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	88.18
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	88.18
PRK10803	263	tol-pal system protein YbgF; Provisional	88.13
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	88.11
PRK03918	880	chromosome segregation protein; Provisional	88.09
PF10482	120	CtIP_N: Tumour-suppressor protein CtIP N-terminal	88.04
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	88.03
PF10226	195	DUF2216: Uncharacterized conserved proteins (DUF22	87.99
KOG2391	365	consensus Vacuolar sorting protein/ubiquitin recep	87.96
PF12808	52	Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2	87.95
PF13747	89	DUF4164: Domain of unknown function (DUF4164)	87.94
PF12777	344	MT: Microtubule-binding stalk of dynein motor; Int	87.8
KOG3650	120	consensus Predicted coiled-coil protein [General f	87.79
smart00340	44	HALZ homeobox associated leucin zipper.	87.78
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	87.78
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	87.74
PLN02320	502	seryl-tRNA synthetase	87.64
PRK14160	211	heat shock protein GrpE; Provisional	87.56
PF12777	344	MT: Microtubule-binding stalk of dynein motor; Int	87.55
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	87.44
PRK14127	109	cell division protein GpsB; Provisional	87.43
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	87.41
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	87.4
PRK05431	425	seryl-tRNA synthetase; Provisional	87.37
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	87.33
PF04999	97	FtsL: Cell division protein FtsL; InterPro: IPR007	87.32
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	87.31
PRK04406	75	hypothetical protein; Provisional	87.24
COG4467	114	Regulator of replication initiation timing [Replic	87.23
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	87.21
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	87.18
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	87.16
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	87.13
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	87.1
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	87.06
KOG0946	970	consensus ER-Golgi vesicle-tethering protein p115	86.97
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	86.96
PRK15396	78	murein lipoprotein; Provisional	86.93
KOG1962	216	consensus B-cell receptor-associated protein and r	86.69
PF13600	104	DUF4140: N-terminal domain of unknown function (DU	86.69
PF13815	118	Dzip-like_N: Iguana/Dzip1-like DAZ-interacting pro	86.63
PF06103	90	DUF948: Bacterial protein of unknown function (DUF	86.52
PRK02119	73	hypothetical protein; Provisional	86.46
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	86.42
PF07889	126	DUF1664: Protein of unknown function (DUF1664); In	86.29
COG4942	420	Membrane-bound metallopeptidase [Cell division and	86.25
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	86.24
cd00632	105	Prefoldin_beta Prefoldin beta; Prefoldin is a hexa	86.2
PF01166	59	TSC22: TSC-22/dip/bun family; InterPro: IPR000580	86.18
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	86.05
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	86.04
PF07407	420	Seadorna_VP6: Seadornavirus VP6 protein; InterPro:	85.81
PF06103	90	DUF948: Bacterial protein of unknown function (DUF	85.8
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	85.78
PF04420	161	CHD5: CHD5-like protein; InterPro: IPR007514 Membe	85.69
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	85.62
PRK00846	77	hypothetical protein; Provisional	85.5
PF08647	96	BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR01395	85.5
COG1792	284	MreC Cell shape-determining protein [Cell envelope	85.5
PRK00295	68	hypothetical protein; Provisional	85.45
PF10883	87	DUF2681: Protein of unknown function (DUF2681); In	85.41
KOG0982	502	consensus Centrosomal protein Nuf [Cell cycle cont	85.41
PRK02224	880	chromosome segregation protein; Provisional	85.38
PF01763	557	Herpes_UL6: Herpesvirus UL6 like; InterPro: IPR002	85.17
COG2919	117	Septum formation initiator [Cell division and chro	85.16
KOG4571	294	consensus Activating transcription factor 4 [Trans	85.14
PRK02793	72	phi X174 lysis protein; Provisional	85.1
PF09744	158	Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; Inte	85.09
COG3879	247	Uncharacterized protein conserved in bacteria [Fun	85.0
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	84.91
PRK14148	195	heat shock protein GrpE; Provisional	84.89
TIGR01834	320	PHA_synth_III_E poly(R)-hydroxyalkanoic acid synth	84.83
PRK03947	140	prefoldin subunit alpha; Reviewed	84.68
PF06698	59	DUF1192: Protein of unknown function (DUF1192); In	84.55
PRK04325	74	hypothetical protein; Provisional	84.5
PF04871	136	Uso1_p115_C: Uso1 / p115 like vesicle tethering pr	84.47
PF09766	355	FimP: Fms-interacting protein; InterPro: IPR019163	84.44
PRK02224	880	chromosome segregation protein; Provisional	84.34
PF14193	83	DUF4315: Domain of unknown function (DUF4315)	84.33
PF02388	406	FemAB: FemAB family; InterPro: IPR003447 The femAB	84.31
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	84.25
PF10018	188	Med4: Vitamin-D-receptor interacting Mediator subu	84.24
COG5493	231	Uncharacterized conserved protein containing a coi	84.16
PF14257	262	DUF4349: Domain of unknown function (DUF4349)	84.11
PF13600	104	DUF4140: N-terminal domain of unknown function (DU	84.1
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	84.0
KOG4348	627	consensus Adaptor protein CMS/SETA [Signal transdu	83.97
PF15188	85	CCDC-167: Coiled-coil domain-containing protein 16	83.91
PF05700	221	BCAS2: Breast carcinoma amplified sequence 2 (BCAS	83.87
PF06785	401	UPF0242: Uncharacterised protein family (UPF0242);	83.77
TIGR00414	418	serS seryl-tRNA synthetase. This model represents	83.72
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	83.68
TIGR02977	219	phageshock_pspA phage shock protein A. Members of	83.63
COG3879	247	Uncharacterized protein conserved in bacteria [Fun	83.61
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	83.57
PF04136	157	Sec34: Sec34-like family ; InterPro: IPR007265 Sec	83.29
PF06657	79	Cep57_MT_bd: Centrosome microtubule-binding domain	83.24
PF14931	120	IFT20: Intraflagellar transport complex B, subunit	83.22
TIGR02338	110	gimC_beta prefoldin, beta subunit, archaeal. Chape	83.19
COG1730	145	GIM5 Predicted prefoldin, molecular chaperone impl	83.16
PRK04863	1486	mukB cell division protein MukB; Provisional	83.15
PF03954	138	Lectin_N: Hepatic lectin, N-terminal domain; Inter	83.0
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	82.94
cd07429	108	Cby_like Chibby, a nuclear inhibitor of Wnt/beta-c	82.88
PF09730	717	BicD: Microtubule-associated protein Bicaudal-D; I	82.87
PF14523	102	Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.	82.87
TIGR01000	457	bacteriocin_acc bacteriocin secretion accessory pr	82.8
PRK04406	75	hypothetical protein; Provisional	82.78
PLN02678	448	seryl-tRNA synthetase	82.78
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	82.5
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	82.46
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	82.26
PF04645	181	DUF603: Protein of unknown function, DUF603; Inter	82.23
PF09730	717	BicD: Microtubule-associated protein Bicaudal-D; I	82.13
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	82.02
KOG3119	269	consensus Basic region leucine zipper transcriptio	81.95
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	81.91
PF08286	118	Spc24: Spc24 subunit of Ndc80; InterPro: IPR013252	81.83
TIGR00293	126	prefoldin, archaeal alpha subunit/eukaryotic subun	81.8
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	81.72
PF10779	71	XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemoly	81.54
PRK09973	85	putative outer membrane lipoprotein; Provisional	81.36
PF10267	395	Tmemb_cc2: Predicted transmembrane and coiled-coil	81.3
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	81.29
PF15458	254	NTR2: Nineteen complex-related protein 2	81.29
PF05103	131	DivIVA: DivIVA protein; InterPro: IPR007793 The Ba	81.26
PRK14127	109	cell division protein GpsB; Provisional	81.22
PF12999	176	PRKCSH-like: Glucosidase II beta subunit-like	81.22
PF08647	96	BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR01395	81.12
KOG4343	655	consensus bZIP transcription factor ATF6 [Transcri	81.12
PF14988	206	DUF4515: Domain of unknown function (DUF4515)	81.01
PF13514	1111	AAA_27: AAA domain	80.99
KOG3647	338	consensus Predicted coiled-coil protein [General f	80.96
PF04822	84	Takusan: Takusan; InterPro: IPR006907 This family	80.95
PRK14161	178	heat shock protein GrpE; Provisional	80.93
KOG3433	203	consensus Protein involved in meiotic recombinatio	80.86
TIGR02680	1353	conserved hypothetical protein TIGR02680. Members	80.86
PRK13923	170	putative spore coat protein regulator protein YlbO	80.78
PF09755	310	DUF2046: Uncharacterized conserved protein H4 (DUF	80.67
PRK04778	569	septation ring formation regulator EzrA; Provision	80.57
PF08738	103	Gon7: Gon7 family; InterPro: IPR014849 In Saccharo	80.47
PF12711	86	Kinesin-relat_1: Kinesin motor; InterPro: IPR02465	80.45
COG5509	65	Uncharacterized small protein containing a coiled-	80.29
COG2841	72	Uncharacterized protein conserved in bacteria [Fun	80.25
PF02050	123	FliJ: Flagellar FliJ protein; InterPro: IPR012823	80.23
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	80.14
KOG3433	203	consensus Protein involved in meiotic recombinatio	80.12
PRK04863	1486	mukB cell division protein MukB; Provisional	80.1
COG5185	622	HEC1 Protein involved in chromosome segregation, i	80.09
PF11544	76	Spc42p: Spindle pole body component Spc42p; InterP	80.03
PF07047	134	OPA3: Optic atrophy 3 protein (OPA3); InterPro: IP	80.01

>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=97.59  E-value=0.00092  Score=46.54  Aligned_cols=55  Identities=35%  Similarity=0.520  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.++.+|-.+|+.+=+.+..|+.++.+|+.+.++|.+++..|+.+-++|.++..+
T Consensus         3 ~E~l~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~   57 (72)
T PF06005_consen    3 LELLEQLEEKIQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNA   57 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            4677777777777777777777777777777666666666666666666655443

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

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=97.59  E-value=0.00081  Score=48.21  Aligned_cols=58  Identities=19%  Similarity=0.452  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      -||.-+.=|+-|+++||+.|..|.++...+...+.+|+.|+..||.|-..-+..|+++
T Consensus        15 qAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~~~WqerLr~L   72 (79)
T PRK15422         15 QAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQAL   72 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555578899999999999999999999999999999999999988887777763

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=97.29  E-value=0.0021  Score=51.17  Aligned_cols=60  Identities=25%  Similarity=0.498  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHHHH---HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           16 LSDVVRMMEQLRTE---AQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        16 L~DAir~lkqLr~e---~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |.|.|++|.+|.+.   .+.|+.+|..|++++..|..+-.+|+.|+..|+.+..-++..+++|
T Consensus        82 l~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L  144 (161)
T TIGR02894        82 LQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTL  144 (161)
T ss_pred             HHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88999999999974   7788889999999998888888888899999988888888888874

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.

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.20  E-value=0.0045  Score=44.14  Aligned_cols=58  Identities=17%  Similarity=0.459  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      -||.-+.=|+-|+++||+.|.+|+.+..++..-+..|+.|+..||.|-..-+..|+++
T Consensus        15 qAvdTI~LLQmEieELKEknn~l~~e~q~~q~~reaL~~eneqlk~e~~~WQerlrsL   72 (79)
T COG3074          15 QAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEEQNGWQERLRAL   72 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555666678999999999999999999999999999999999999988777777763

>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=97.11  E-value=0.0095  Score=41.46  Aligned_cols=46  Identities=28%  Similarity=0.514  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      .-||.-+.-|+.|+++||++|..|.++...|+.|-+.|++|...-+
T Consensus        14 ~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~   59 (72)
T PF06005_consen   14 QQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQ   59 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555566677777777777766555555544444444444333

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.

>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=96.95  E-value=0.0075  Score=45.56  Aligned_cols=53  Identities=32%  Similarity=0.574  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      -.+.+|..|.+++.++..++..|++++..|..+|++|++|..+|-.+.+.++.
T Consensus        13 ~~~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~~~   65 (120)
T PF12325_consen   13 PSVQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEELRA   65 (120)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45789999999999999999999999999999999999998877776666543

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 [].

>smart00353 HLH helix loop helix domain

Probab=96.78  E-value=0.0019  Score=40.20  Aligned_cols=25  Identities=32%  Similarity=0.375  Sum_probs=22.9

Q ss_pred             CCCCchhhhHHHHHHHHHHHHHHHH
Q 032660            7 PPKTDKATILSDVVRMMEQLRTEAQ   31 (136)
Q Consensus         7 p~K~DKAsIL~DAir~lkqLr~e~~   31 (136)
                      ..|.||++||.+|+.|++.|+.+++
T Consensus        28 ~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353       28 NKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            4799999999999999999998875

>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=96.73  E-value=0.0065  Score=46.56  Aligned_cols=55  Identities=29%  Similarity=0.564  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHH--HHHHHHHHHhHHHHHHHHHHHHhccC
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEK--NELRDEKQRLKADKEKLEQQVKAMSA   77 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EK--nELrdEk~~Lk~eke~Le~qlk~~~~   77 (136)
                      +++|+.|+..|+.++..|+++.+.|..+-  .||+++...|+.|++.|+..|..+..
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            77888888888888888888888877766  68899999999999999999998754

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 [].

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=96.53  E-value=0.017  Score=52.54  Aligned_cols=52  Identities=29%  Similarity=0.450  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHH---------------HHHHHHHHHHHhHHHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKA---------------EKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~---------------EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      +--+|++|.++++|..+|+.|.+|++.|+.               |+.||.+|...|+.+..+++.+
T Consensus        65 va~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~  131 (472)
T TIGR03752        65 VAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGL  131 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence            335789999999999999999888877754               4455555555555554444433

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.

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=96.45  E-value=0.03  Score=40.24  Aligned_cols=55  Identities=29%  Similarity=0.422  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ..++.+|-+.|+.-=+.+.-|+-|+.+||.+.+.|.+|...+++..+.|+++-+.
T Consensus         3 ~EvleqLE~KIqqAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~q   57 (79)
T PRK15422          3 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNH   57 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            4689999999999999999999999999999999999988876666666655443

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=96.28  E-value=0.045  Score=37.80  Aligned_cols=55  Identities=20%  Similarity=0.330  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      =|.+|-...++|+.+|..|.++...+..|+..|.+.+..-.+.+|.+=..|++|-
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            3677888889999999999999999999999999999888888888888888763

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.

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

Probab=96.25  E-value=0.0057  Score=38.53  Aligned_cols=24  Identities=29%  Similarity=0.339  Sum_probs=22.1

Q ss_pred             CCCCchhhhHHHHHHHHHHHHHHH
Q 032660            7 PPKTDKATILSDVVRMMEQLRTEA   30 (136)
Q Consensus         7 p~K~DKAsIL~DAir~lkqLr~e~   30 (136)
                      ..|.||++||..|+.||+.|+.++
T Consensus        36 ~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083          36 SKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHh
Confidence            379999999999999999999875

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

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=96.18  E-value=0.074  Score=41.03  Aligned_cols=72  Identities=25%  Similarity=0.473  Sum_probs=65.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCCCCCCCCC
Q 032660           14 TILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLPHP   85 (136)
Q Consensus        14 sIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~~p~f~ph~   85 (136)
                      ...+.+++.|...|.....+..++..+..++.....+.+++|++...++.+.+++..+...+...-|.+..|
T Consensus        70 ~~~~~~v~~L~h~keKl~~~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~~~~~~~l~~~~~~~~~P  141 (177)
T PF13870_consen   70 KKIGKTVQILTHVKEKLHFLSEELERLKQELKDREEELAKLREELYRVKKERDKLRKQNKKLRQQGGLLGVP  141 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCc
Confidence            346789999999999999999999999999999999999999999999999999999999987766655544

>smart00338 BRLZ basic region leucin zipper

Probab=96.15  E-value=0.025  Score=37.27  Aligned_cols=36  Identities=28%  Similarity=0.533  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      ++.+|..+++.|..+|..|..++..|..|...|+++
T Consensus        27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~   62 (65)
T smart00338       27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSE   62 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555555555555555555554444444444443

>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=96.11  E-value=0.031  Score=36.84  Aligned_cols=38  Identities=37%  Similarity=0.598  Sum_probs=18.8

Q ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           35 QSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        35 ~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      .....|++++..|+.|...|+.+...|+.++..|..++
T Consensus        26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~   63 (64)
T PF00170_consen   26 QYIEELEEKVEELESENEELKKELEQLKKEIQSLKSEN   63 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            34444444455555555555555555555555554443

; 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 ....

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

Probab=96.10  E-value=0.051  Score=46.36  Aligned_cols=58  Identities=28%  Similarity=0.543  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |--+..-+++...+.+.++++.|.++..+|..|-||++++..+|+.|+.+|+..++.+
T Consensus       132 d~ke~~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l  189 (290)
T COG4026         132 DLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKL  189 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            5555566777778888888889999999999999999999888888888888887764

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

Probab=96.09  E-value=0.031  Score=47.63  Aligned_cols=45  Identities=38%  Similarity=0.612  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      .++..++++|+.+...|.++++.|..|+.+|.+|...|+.+.+.|
T Consensus        46 ~~~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l   90 (314)
T PF04111_consen   46 EELEEELEKLEQEEEELLQELEELEKEREELDQELEELEEELEEL   90 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444455555555555554444444444444444444444443

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.

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

Probab=96.05  E-value=0.05  Score=40.35  Aligned_cols=52  Identities=29%  Similarity=0.495  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      +|-..+..|.+....|.+++..||..-.+|-+||++|+-|-+.|...|....
T Consensus         5 ~l~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~   56 (107)
T PF06156_consen    5 ELFDRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELE   56 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5556666677777777777777777777777777777777777777666643

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

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.00  E-value=0.065  Score=45.63  Aligned_cols=63  Identities=22%  Similarity=0.429  Sum_probs=49.0

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           12 KATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        12 KAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +=+.|.++-.=++++..|+++|-...+.++.++.+++.|-+++..|...|+.+|+.|+..+..
T Consensus        36 ~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~~   98 (265)
T COG3883          36 QDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVE   98 (265)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345667777778888888888888888888888888888888888888888888777766554

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

Probab=95.96  E-value=0.011  Score=37.53  Aligned_cols=22  Identities=32%  Similarity=0.487  Sum_probs=19.9

Q ss_pred             CCCCCchhhhHHHHHHHHHHHH
Q 032660            6 RPPKTDKATILSDVVRMMEQLR   27 (136)
Q Consensus         6 rp~K~DKAsIL~DAir~lkqLr   27 (136)
                      ...|.||++||..||.||++|+
T Consensus        34 ~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen   34 SSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             TTSSSSHHHHHHHHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHHHHHhC
Confidence            4478999999999999999985

; 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 ....

>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=95.93  E-value=0.027  Score=36.10  Aligned_cols=38  Identities=39%  Similarity=0.518  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      ||-..-.-||..+.+|..+...|..|+.+|+.|...|+
T Consensus         2 QlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~   39 (45)
T PF02183_consen    2 QLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELK   39 (45)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555555555555555555555555554444443

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

>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=95.93  E-value=0.091  Score=39.22  Aligned_cols=59  Identities=24%  Similarity=0.480  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH----HHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELK----AEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~----~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +++|.-|..||.+.+.++..+..|+.+....+    ..+....+++..|+.+++.++..+..+
T Consensus        55 a~~~~~L~~lr~e~~~~~~~~~~l~~~~~~a~~~l~~~e~sw~~qk~~le~e~~~~~~r~~dL  117 (132)
T PF07926_consen   55 AEDIKELQQLREELQELQQEINELKAEAESAKAELEESEASWEEQKEQLEKELSELEQRIEDL  117 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            57789999999999999999999988865443    333344445555666655555554443

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

>PRK10884 SH3 domain-containing protein; Provisional

Probab=95.91  E-value=0.064  Score=43.63  Aligned_cols=54  Identities=20%  Similarity=0.349  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHH-----------HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQE-----------KIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~e-----------e~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ..|..|..|+++|+++...+..           +....+.+.++|++|++.|+.+.+.+++++..
T Consensus        93 ~rlp~le~el~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~  157 (206)
T PRK10884         93 TRVPDLENQVKTLTDKLNNIDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDA  157 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555444444333           33333334444566666555555555555443

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

Probab=95.79  E-value=0.016  Score=46.21  Aligned_cols=46  Identities=28%  Similarity=0.485  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      |.|+-+..+.-=+.|.-|++|+    .||..||.|.++||-|...|.+++
T Consensus         2 LeD~EsklN~AIERnalLE~EL----dEKE~L~~~~QRLkDE~RDLKqEl   47 (166)
T PF04880_consen    2 LEDFESKLNQAIERNALLESEL----DEKENLREEVQRLKDELRDLKQEL   47 (166)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHCH--------------
T ss_pred             HHHHHHHHHHHHHHhHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5677888888888999999999    788899999999999988888887

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.

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=95.63  E-value=0.093  Score=49.91  Aligned_cols=96  Identities=25%  Similarity=0.446  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc---cCCCCCCCC---CCCCchhhhhh
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM---SAPSGFLPH---PSSMSAAFAAQ   95 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~---~~~p~f~ph---~~~~p~a~aa~   95 (136)
                      -|.+|.+.-|+|..+++.+..+|.+||.+.-.-+-|..+||.+||.-|.|++.+   |.|--|+|-   |-.+|+.-.+.
T Consensus        94 EL~ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El~~~n~pkl~LP~sllP~~~pr~l~pp  173 (907)
T KOG2264|consen   94 ELTELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEELRETNNPKLFLPFSLLPLQIPRELEPP  173 (907)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHHHhhcCCceeeccccCcccCcccCCCc
Confidence            356677777777788888888888888888888888899999999999998885   333334443   12334333344


Q ss_pred             hhhccCcccccCCCC------Ccccccc
Q 032660           96 SQVASNKLVPFIGYP------GVAMWQF  117 (136)
Q Consensus        96 ~qa~~~k~~p~~~yp------g~~mWq~  117 (136)
                      .|+++.-+--+..|.      |||.+-|
T Consensus       174 ~~~~~c~lhncfdySRCsltSgfPVYvy  201 (907)
T KOG2264|consen  174 SQISPCQLHNCFDYSRCSLTSGFPVYVY  201 (907)
T ss_pred             cccCcccchhccccccccccCCceeEEe
Confidence            466666665555663      5555544

>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=95.61  E-value=0.2  Score=35.72  Aligned_cols=47  Identities=30%  Similarity=0.420  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      -=..|..|+..|..+...|.+.+..++.|..-|+.||..|..=|++|
T Consensus        17 ~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nL   63 (80)
T PF10224_consen   17 EKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNL   63 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34578889999999999999999999999999999999999999988

The exact function is unknown.

>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=95.53  E-value=0.15  Score=35.27  Aligned_cols=60  Identities=30%  Similarity=0.463  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |.+-=..|.+|+.|-++|....-.+...|+.|.+.-.++..+...|+..+++++.++..+
T Consensus         7 l~EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l   66 (74)
T PF12329_consen    7 LAEKDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESL   66 (74)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334445788999999999999999999999999888888888888888888888877664

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.

>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=95.48  E-value=0.11  Score=34.22  Aligned_cols=36  Identities=28%  Similarity=0.576  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      ++.+|..++..|..+|..|.+++..|+.+...|+.+
T Consensus        27 ~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e   62 (64)
T PF00170_consen   27 YIEELEEKVEELESENEELKKELEQLKKEIQSLKSE   62 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            556666666666666666666666655555555544

; 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 ....

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

Probab=95.40  E-value=0.099  Score=44.26  Aligned_cols=50  Identities=28%  Similarity=0.468  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      |..||.++..++.+++.++.++.+|+.++++++++...++.++.+++.++
T Consensus       211 L~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI  260 (325)
T PF08317_consen  211 LEALRQELAEQKEEIEAKKKELAELQEELEELEEKIEELEEQKQELLAEI  260 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444444443333333333333333

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

Probab=95.35  E-value=0.14  Score=36.32  Aligned_cols=52  Identities=31%  Similarity=0.533  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHH---HHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKA---EKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~---EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .++|+.+++.|+.+...+..++..++.   +..+|.+|-..++.++..++.++..
T Consensus        38 ~r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~   92 (108)
T PF02403_consen   38 RRELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKE   92 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456777888888888888888776665   4566666666666666666666555

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 ....

>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=95.26  E-value=0.12  Score=40.12  Aligned_cols=50  Identities=32%  Similarity=0.497  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +..+++.-|+++..|++++..++.+.|.|+.|-..|.+|++.|.++++-+
T Consensus        43 ~~~daEn~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~   92 (140)
T PF10473_consen   43 LILDAENSKAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKK   92 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44566677888888999999999999999999999999999998888775

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

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=95.21  E-value=0.11  Score=41.61  Aligned_cols=55  Identities=25%  Similarity=0.363  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      .....+.|+.|.++|+.++..|+++++.|..|.++|..+...++.|-+-|=+-+.
T Consensus        95 ~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~Im~  149 (161)
T TIGR02894        95 TNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDIMD  149 (161)
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445667788888888888888888888888888888888888877776655443

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.

>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=95.18  E-value=0.16  Score=38.44  Aligned_cols=60  Identities=25%  Similarity=0.410  Sum_probs=38.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH---HhHHHHHHHHHHHHh
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQ---RLKADKEKLEQQVKA   74 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~---~Lk~eke~Le~qlk~   74 (136)
                      ++.-=-.-|+++.+|+..|+.++..|+.+...+..|.-.|..++.   .+..+...|+.+++.
T Consensus        17 ~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~~~~~~~~~~L~~el~~   79 (120)
T PF12325_consen   17 LVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEELRALKKEVEELEQELEE   79 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333334457788888888888888888777777777766666653   333444455555544

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 [].

>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=95.17  E-value=0.087  Score=33.72  Aligned_cols=39  Identities=28%  Similarity=0.549  Sum_probs=19.6

Q ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           33 LKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        33 Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      |...++.|......|+.+-..|..||..|++++..|...
T Consensus         3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~k   41 (45)
T PF02183_consen    3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEK   41 (45)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344445555555555555555555555555555554443

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

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

Probab=95.15  E-value=0.099  Score=44.66  Aligned_cols=46  Identities=37%  Similarity=0.582  Sum_probs=29.7

Q ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           30 AQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        30 ~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .-.||+..+.+.++..++..||.||++|+..|+++.+.++..|+.+
T Consensus       130 ~~d~ke~~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~l  175 (290)
T COG4026         130 YMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRL  175 (290)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3355666666666666666666666666666666666666666664

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.15  E-value=0.23  Score=35.55  Aligned_cols=54  Identities=30%  Similarity=0.427  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      ..++.+|...++.--+.+.-|+-++.+||.++|.|..|-+.+....|.|+.+-.
T Consensus         3 lEv~ekLE~KiqqAvdTI~LLQmEieELKEknn~l~~e~q~~q~~reaL~~ene   56 (79)
T COG3074           3 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERENE   56 (79)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHH
Confidence            468889999999999999999999999999999999999988888888875433

>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=95.10  E-value=0.1  Score=39.99  Aligned_cols=54  Identities=26%  Similarity=0.541  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH--HHhHHHHHHHHHHHHhcc
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEK--QRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk--~~Lk~eke~Le~qlk~~~   76 (136)
                      +.+|..++..|++++..|..+++.|..|.+.|+.+-  ..|...|+.|+.+++.+.
T Consensus        74 l~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~  129 (169)
T PF07106_consen   74 LAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELE  129 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHH
Confidence            556666666666666666666666666666666554  356667777777766654

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=95.04  E-value=0.19  Score=37.70  Aligned_cols=51  Identities=22%  Similarity=0.381  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +|-..+..|......|.+++..||..-.+|-+||++|+-|-+.|...|..+
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            444555556666666666666666666666666666666666666555554

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=95.03  E-value=0.21  Score=42.93  Aligned_cols=61  Identities=21%  Similarity=0.316  Sum_probs=53.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           14 TILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        14 sIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +-..+-=..|+||..|-++|..+|..|++..+.|-++-+||+.+..-|..+.-++.+|-+.
T Consensus        90 aRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~~~~~~~  150 (292)
T KOG4005|consen   90 ARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELDSELELLRQELAELKQQQQH  150 (292)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHHHHHH
Confidence            3344555678999999999999999999999999999999999999999999999887655

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.98  E-value=0.14  Score=43.67  Aligned_cols=66  Identities=26%  Similarity=0.462  Sum_probs=51.1

Q ss_pred             hhhhHHH----HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccC
Q 032660           12 KATILSD----VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA   77 (136)
Q Consensus        12 KAsIL~D----Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~   77 (136)
                      ++.+++|    .=.-++++..+.+.+..++++|...+.++..+.+++++|...+++++.+|+.++..+..
T Consensus        25 ~a~~~~~~i~~~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~   94 (265)
T COG3883          25 FAALLSDKIQNQDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKE   94 (265)
T ss_pred             hhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444    33457788888888888888888888888888888888888888888888888887643

>PRK11637 AmiB activator; Provisional

Probab=94.92  E-value=0.26  Score=42.79  Aligned_cols=59  Identities=12%  Similarity=0.248  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.++..-+++|..+++.+..++..++.++..+..+.++|+++...++.+++.++.+|+.
T Consensus        70 ~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~~  128 (428)
T PRK11637         70 RASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLAA  128 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444445555555555555555555555555555555555555555555554444

>PRK11637 AmiB activator; Provisional

Probab=94.79  E-value=0.28  Score=42.63  Aligned_cols=37  Identities=32%  Similarity=0.398  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           38 EDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ..+++++..+..+.+++..+...|+.+|..++.++..
T Consensus        85 ~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~  121 (428)
T PRK11637         85 SQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAA  121 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333344444444444444444333

>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=94.70  E-value=0.2  Score=33.02  Aligned_cols=47  Identities=36%  Similarity=0.562  Sum_probs=29.4

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      ..+..+++.+...|+.++..++.|..+|+.|...|+.+.+.++..-+
T Consensus        16 ~~~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~AR   62 (80)
T PF04977_consen   16 YSRYYQLNQEIAELQKEIEELKKENEELKEEIERLKNDPDYIEKVAR   62 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            34445555666666666666666666666677777666666666655

These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle

>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=94.63  E-value=0.26  Score=40.80  Aligned_cols=50  Identities=18%  Similarity=0.349  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      -.+|.+++.|.+.|..|.....|+++...+.+|.|......+++|.++.+
T Consensus        31 e~~L~e~~kE~~~L~~Er~~h~eeLrqI~~DIn~lE~iIkqa~~er~~~~   80 (230)
T PF10146_consen   31 EKCLEEYRKEMEELLQERMAHVEELRQINQDINTLENIIKQAESERNKRQ   80 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35788888888888888887777765555555555444444444444333

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.

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

Probab=94.63  E-value=0.38  Score=37.82  Aligned_cols=56  Identities=29%  Similarity=0.439  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      --.-|.+|+.++..|+..+..|.+++++...--.-|+||...|..+..-+|.+++.
T Consensus       114 ~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~  169 (194)
T PF08614_consen  114 KERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQLNMLEEKLRK  169 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33445556666666666666666665555555555666666555555555555443

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=94.63  E-value=0.38  Score=33.13  Aligned_cols=52  Identities=21%  Similarity=0.410  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHH-------HHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKN-------ELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKn-------ELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.-||.....+-..++..+.+++.|..|++       +..+++..|++|.+.|..+++.
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            455677777777777777777777777764       4567777888888888888765

>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=94.56  E-value=0.2  Score=33.07  Aligned_cols=36  Identities=31%  Similarity=0.412  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR   55 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELr   55 (136)
                      +.-+.+++.|++.|+.+++.++.++.+|+.|.+.|+
T Consensus        16 ~~~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~   51 (80)
T PF04977_consen   16 YSRYYQLNQEIAELQKEIEELKKENEELKEEIERLK   51 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            344567888888888888888888888888888883

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

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

Probab=94.56  E-value=0.33  Score=43.17  Aligned_cols=45  Identities=38%  Similarity=0.469  Sum_probs=33.0

Q ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           32 KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      +.+++.+.++.+..+|+.-..||+.-++.|+.++|+||+|+..|+
T Consensus       222 r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~  266 (365)
T KOG2391|consen  222 RREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQ  266 (365)
T ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence            455667777777777777777777777778888888887777653

>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=94.55  E-value=0.12  Score=47.93  Aligned_cols=38  Identities=32%  Similarity=0.520  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           39 DLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        39 ~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      .|+...+-+..||.+|++||+.|+..+++|+..|..++
T Consensus       421 Elks~lrv~qkEKEql~~EkQeL~~yi~~Le~r~~~~~  458 (546)
T PF07888_consen  421 ELKSSLRVAQKEKEQLQEEKQELLEYIERLEQRLDKVA  458 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            34445566678999999999999999999999999863

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 [].

>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=94.53  E-value=0.15  Score=32.42  Aligned_cols=48  Identities=27%  Similarity=0.349  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      ..|..+.+.|..++..++.....=..+-..|+-+|..||.+|.++..|
T Consensus         2 ~~L~~~h~~Ld~~I~~~e~~~~~~d~~l~~LKk~kL~LKDei~~ll~q   49 (49)
T PF04325_consen    2 ARLFEEHHELDKEIHRLEKRPEPDDEELERLKKEKLRLKDEIYRLLRQ   49 (49)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT--S-HHHHHHHHHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            456777777777777776654444455667778888888888777654

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

>PRK09039 hypothetical protein; Validated

Probab=94.52  E-value=0.32  Score=41.93  Aligned_cols=56  Identities=11%  Similarity=0.133  Sum_probs=49.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           14 TILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        14 sIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      ++.+++-+-|..|+.||+.||+.+..|++.+...+.+..+.+.....|+.++++.=
T Consensus       130 ~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~  185 (343)
T PRK09039        130 QVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVAL  185 (343)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57788999999999999999999999999999999888888888888887777663

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

Probab=94.48  E-value=0.18  Score=44.19  Aligned_cols=60  Identities=18%  Similarity=0.266  Sum_probs=34.4

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCCC
Q 032660           13 ATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS   79 (136)
Q Consensus        13 AsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~~p   79 (136)
                      |++-+-+..-.++|..+..+|+.++..|+.+.++++.+.+.++.       |+++++.+++.+..+|
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~   66 (398)
T PTZ00454          7 AAVASSTTHTERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKR-------ELIRAKEEVKRIQSVP   66 (398)
T ss_pred             ccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCC
Confidence            34444444555666666666666666666666666655555554       5555555555555555

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=94.45  E-value=0.25  Score=40.26  Aligned_cols=40  Identities=25%  Similarity=0.501  Sum_probs=18.8

Q ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           30 AQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        30 ~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      ..+|+++|+.|++|+.+|+.+..+++    .|+.|-++|...|.
T Consensus        71 ~~~l~~en~~L~~e~~~l~~~~~~~~----~l~~en~~L~~lL~  110 (276)
T PRK13922         71 LFDLREENEELKKELLELESRLQELE----QLEAENARLRELLN  110 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHhc
Confidence            34455555555555555555554331    33444444444443

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.45  E-value=0.48  Score=38.56  Aligned_cols=32  Identities=19%  Similarity=0.223  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           40 LQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        40 L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      ....+.+|+.|..+|++|...++++.+.|+.+
T Consensus       130 ~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~  161 (206)
T PRK10884        130 SDSVINGLKEENQKLKNQLIVAQKKVDAANLQ  161 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333334444444444444444444444333

>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=94.42  E-value=0.29  Score=39.74  Aligned_cols=42  Identities=21%  Similarity=0.332  Sum_probs=17.6

Q ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           33 LKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        33 Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |..++..|..++..|+...+.|......++.++++|+.|+..
T Consensus        54 L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~~   95 (251)
T PF11932_consen   54 LLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIEQ   95 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333334444444445555554444

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.

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

Probab=94.39  E-value=0.4  Score=40.61  Aligned_cols=54  Identities=26%  Similarity=0.385  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +-.-|.++..+++.+|.+...|+.+...++.+.+++.++++.++++|.+++..+
T Consensus       214 lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~  267 (325)
T PF08317_consen  214 LRQELAEQKEEIEAKKKELAELQEELEELEEKIEELEEQKQELLAEIAEAEKIR  267 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334445555555555555555555555555555555555555555555554433

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=94.37  E-value=0.4  Score=39.38  Aligned_cols=52  Identities=29%  Similarity=0.433  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      .+.=|-|-.|+++||.....|+|+.+.|-+....|..|++.|-++++.|+.+
T Consensus        59 l~~aK~l~eEledLk~~~~~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqee  110 (193)
T PF14662_consen   59 LQKAKALEEELEDLKTLAKSLEEENRSLLAQARQLEKEQQSLVAEIETLQEE  110 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333334445555555555555555555554444455555554444444444

>COG5570 Uncharacterized small protein [Function unknown]

Probab=94.37  E-value=0.16  Score=34.44  Aligned_cols=46  Identities=30%  Similarity=0.446  Sum_probs=37.9

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHH-------HHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           27 RTEAQKLKQSTEDLQEKIKELK-------AEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~-------~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      -+-+..|...+..|+++|++-.       .+..||.-.|.+||.+||+|..|.
T Consensus         4 eshl~eL~kkHg~le~ei~ea~n~Ps~dd~~i~eLKRrKL~lKeeIEkLka~~   56 (57)
T COG5570           4 ESHLAELEKKHGNLEREIQEAMNSPSSDDLAIRELKRRKLRLKEEIEKLKAQM   56 (57)
T ss_pred             HHHHHHHHHhhchHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHHHHHhccC
Confidence            4567788888999999987764       467899999999999999998763

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=94.26  E-value=0.22  Score=45.53  Aligned_cols=54  Identities=28%  Similarity=0.472  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHH---------------HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           23 MEQLRTEAQKLKQSTEDLQE---------------KIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~e---------------e~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      +..|.+|-++|+++|+.|+.               +.+++..|...|.+|.+.|+..+..|+.||..+.
T Consensus        75 ~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~~l~~~~  143 (472)
T TIGR03752        75 LAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQRRLAGVL  143 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            45567777788888888865               3578899999999999999999999999987653

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.

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

Probab=94.25  E-value=0.38  Score=38.32  Aligned_cols=55  Identities=33%  Similarity=0.567  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHH------HHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELK------AEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~------~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +-+..|+.+++++++++..|++++...+      .|+.++-++...|+.++.+|+.+|+..
T Consensus        69 ~~~~~l~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~~~  129 (188)
T PF03962_consen   69 NKLEKLQKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKELEKY  129 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456677777777777777777765554      456667777888888888888888754

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

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

Probab=94.23  E-value=0.36  Score=44.88  Aligned_cols=66  Identities=27%  Similarity=0.431  Sum_probs=58.0

Q ss_pred             CCchhhhH---HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660            9 KTDKATIL---SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus         9 K~DKAsIL---~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +..+.++-   .+.-+-+.+|+.++++|+.+.+.+.++++.++.+..++.+|....+.+.++|+++++-
T Consensus       313 ~~~~~~~~~~~~~~~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~l  381 (594)
T PF05667_consen  313 PKEKETEEDEQEEQEQELEELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELKL  381 (594)
T ss_pred             cccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444443   4667889999999999999999999999999999999999999999999999999886

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

Probab=94.19  E-value=0.15  Score=44.64  Aligned_cols=42  Identities=26%  Similarity=0.375  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      ..++.|+.+++.|+..+..|+++.+.++.|.+.|++|...|+
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (398)
T PTZ00454         22 EKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQ   63 (398)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            446678889999999999999999999998888888766553

>PF15294 Leu_zip: Leucine zipper

Probab=94.11  E-value=0.19  Score=43.04  Aligned_cols=46  Identities=30%  Similarity=0.525  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      =|..|+.+|+++|++|.+.++.+.......-+||..|++++..|+.
T Consensus       129 ll~kEi~rLq~EN~kLk~rl~~le~~at~~l~Ek~kl~~~L~~lq~  174 (278)
T PF15294_consen  129 LLNKEIDRLQEENEKLKERLKSLEKQATSALDEKSKLEAQLKELQD  174 (278)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3678999999999999999999999999999999999999988887

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

Probab=94.01  E-value=0.62  Score=35.77  Aligned_cols=59  Identities=24%  Similarity=0.500  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.+.-..+.+|..|...+...+..++.+...++....++++++...+...+.++..++.
T Consensus        83 ~~~~~~~l~~l~~el~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~  141 (191)
T PF04156_consen   83 LSELQQQLQQLQEELDQLQERIQELESELEKLKEDLQELRELLKSVEERLDSLDESIKE  141 (191)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            34555556666666666666666666555555555555555555544444444444443

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 [].

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=93.99  E-value=0.56  Score=35.15  Aligned_cols=49  Identities=27%  Similarity=0.399  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      -|.+|-.++..|-++.+.|...+.+|-.|-.+||-||..|+.-++++++
T Consensus         9 ~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~   57 (110)
T PRK13169          9 ALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA   57 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3555666666666666666666666666666666777777666666533

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

Probab=93.93  E-value=0.52  Score=32.91  Aligned_cols=52  Identities=25%  Similarity=0.363  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHH--------HHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKN--------ELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKn--------ELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |++.-.++.+|+.+|=+|.=+|..|...-+        ++..|+..||.+++.|..+++.
T Consensus         2 lrEqe~~i~~L~KENF~LKLrI~fLee~l~~~~~~~~~~~~keNieLKve~~~L~~el~~   61 (75)
T PF07989_consen    2 LREQEEQIDKLKKENFNLKLRIYFLEERLQKLGPESIEELLKENIELKVEVESLKRELQE   61 (75)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567777888888888888777776665554        3455555666666666655554

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=93.90  E-value=0.4  Score=43.86  Aligned_cols=59  Identities=17%  Similarity=0.342  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      +...-|.+-+..+.+|+++.+.|+.|.+.++..+.+++.+...|++|+.+|+.|++++.
T Consensus        66 VnqSALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~  124 (475)
T PRK13729         66 VRQHATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALG  124 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhh
Confidence            34456666677777888888888877787888888888888899999999999987753

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=93.86  E-value=0.48  Score=38.89  Aligned_cols=57  Identities=23%  Similarity=0.420  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccC
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA   77 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~   77 (136)
                      ..++-|..+-.+|-+.+..++.+.+.|.++.-.|++||..|..+.+.++.+.+.++.
T Consensus        74 ~~~~~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk~~~~eL~~  130 (193)
T PF14662_consen   74 TLAKSLEEENRSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGLKKRSKELAT  130 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHH
Confidence            344444444445555555555666667777777777777777777777777666543

>smart00338 BRLZ basic region leucin zipper

Probab=93.74  E-value=0.4  Score=31.48  Aligned_cols=38  Identities=34%  Similarity=0.630  Sum_probs=21.3

Q ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           35 QSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        35 ~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      .....|+.++..|+.|..+|+.+...|+.++..|.+++
T Consensus        26 ~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~   63 (65)
T smart00338       26 AEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL   63 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34455555555555555555555555555555555544

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

Probab=93.69  E-value=0.45  Score=39.93  Aligned_cols=54  Identities=30%  Similarity=0.427  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.+++|..|++.++....+|+.++..|..+..+|+++...|+..+.+++..+-.
T Consensus        89 ~e~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l~~~~~~~e~~~~e  142 (239)
T COG1579          89 RELRALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLERLEKNLAE  142 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567888888888888888888888888888888888888888888877776655

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

Probab=93.66  E-value=0.51  Score=36.75  Aligned_cols=49  Identities=29%  Similarity=0.494  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHH-HHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           26 LRTEAQKLKQSTEDLQEKIKEL-KAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L-~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +..+...++.....|..++..+ +.+.++||.+...|+.|+++|+++|+.
T Consensus        49 ~e~~~~~~~a~~~eLr~el~~~~k~~~~~lr~~~e~L~~eie~l~~~L~~   98 (177)
T PF07798_consen   49 LENQEYLFKAAIAELRSELQNSRKSEFAELRSENEKLQREIEKLRQELRE   98 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333344444444444444322 344556666666666666666665554

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

Probab=93.65  E-value=0.64  Score=34.46  Aligned_cols=57  Identities=32%  Similarity=0.501  Sum_probs=38.2

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           10 TDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        10 ~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      |||-.|.    .-|.+|-.++..|-++.+.|...+.+|-.|=.+||-|+..|+.-+.++++
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            4554443    34566666777777777777777777777777777777777777766665

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

>TIGR02209 ftsL_broad cell division protein FtsL

Probab=93.63  E-value=0.96  Score=30.56  Aligned_cols=48  Identities=25%  Similarity=0.379  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      ..+.++..+..+..+++.++.+++.|-++|+.|...|.+ .++++.--+
T Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~-~~rIe~~Ar   68 (85)
T TIGR02209        21 SAQHQTRQLNNELQKLQLEIDKLQKEWRDLQLEVAELSR-HERIEKIAK   68 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-HHHHHHHHH
Confidence            344555566666666666666666666666666666654 455555433

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.

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=93.62  E-value=0.27  Score=35.97  Aligned_cols=45  Identities=18%  Similarity=0.299  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ..+|+.|++.++++|+.|+.+...|.       +|...|+.+.+=+|.+-+.
T Consensus        29 ~~~l~~q~~~~~~e~~~l~~~n~~L~-------~eI~~L~~~~dyiEe~AR~   73 (105)
T PRK00888         29 YWRVNDQVAAQQQTNAKLKARNDQLF-------AEIDDLKGGQEAIEERARN   73 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHhhCcHHHHHHHHHH
Confidence            44555555555555555555554444       4444454444556655554

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

Probab=93.60  E-value=0.48  Score=39.56  Aligned_cols=61  Identities=18%  Similarity=0.401  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccC
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA   77 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~   77 (136)
                      ++.-.+|-=+.+|=.+.|..|..|+++.+.+..+..+||.|...|++|-.+|=..++-+.+
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            4666778888999999999999999999999999999999999999999999999888744

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

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

Probab=93.42  E-value=0.49  Score=44.18  Aligned_cols=55  Identities=25%  Similarity=0.480  Sum_probs=36.5

Q ss_pred             HHHHHHHHH----HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           21 RMMEQLRTE----AQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        21 r~lkqLr~e----~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ..|+||+.|    ++.||.++..+++++..+..+.+.|++||...-..+..|+.+|..+
T Consensus         4 e~l~qlq~Erd~ya~~lk~e~a~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~eL   62 (617)
T PF15070_consen    4 ESLKQLQAERDQYAQQLKEESAQWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSEL   62 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355666655    4566677777777777777777777777776666666666666554

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=93.35  E-value=0.28  Score=40.90  Aligned_cols=48  Identities=25%  Similarity=0.354  Sum_probs=41.6

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR   55 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELr   55 (136)
                      .|..||.||--+|.|+.+|..++.+-.++...|+.+.-.|+.=||+-.
T Consensus        99 ~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~vtAL~iIk~~YE  146 (229)
T KOG1319|consen   99 QKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKDVTALKIIKVNYE  146 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478899999999999999999999998888888888877777777654

>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=93.35  E-value=0.44  Score=41.53  Aligned_cols=51  Identities=25%  Similarity=0.464  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +|-.++++++..++.|+.+.+.+.-||.|+..|....+.-.+||++||..+
T Consensus       130 ~lV~qLEk~~~q~~qLe~d~qs~lDEkeEl~~ERD~yk~K~~RLN~ELn~~  180 (319)
T PF09789_consen  130 DLVEQLEKLREQIEQLERDLQSLLDEKEELVTERDAYKCKAHRLNHELNYI  180 (319)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666999999999999999999999999999999999999999999874

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

Probab=93.32  E-value=1.1  Score=36.75  Aligned_cols=54  Identities=22%  Similarity=0.481  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHH----HHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELK----AEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~----~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      .-+-+..|+.++..|+..|..|+..+.+|.    .+...+......|++++..+..++
T Consensus       221 ~r~~~~~l~~el~~l~~~~~~Le~~l~~le~~~~~~~~~~~~~i~~le~el~~l~~~~  278 (312)
T PF00038_consen  221 LRRQIQSLQAELESLRAKNASLERQLRELEQRLDEEREEYQAEIAELEEELAELREEM  278 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhhhHhhhhhhccccchhhhhhhHHHHHHHHHHHHHHHHHhhhccchhHHHHHHHH
Confidence            334455555666666666666666655443    233333333344444444444333

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 ....

>PHA02562 46 endonuclease subunit; Provisional

Probab=93.28  E-value=0.7  Score=40.45  Aligned_cols=55  Identities=18%  Similarity=0.257  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      |.+.++-.++|++++++|+..+..+.++++.|..+.+++++++..+..++.+.+.
T Consensus       353 i~~~~~~~~~l~~ei~~l~~~~~~~~~~l~~l~~~l~~~~~~~~~~~ke~~~~~~  407 (562)
T PHA02562        353 LITLVDKAKKVKAAIEELQAEFVDNAEELAKLQDELDKIVKTKSELVKEKYHRGI  407 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666677777777777777777777777777777777777777777666543

>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=93.24  E-value=0.43  Score=40.61  Aligned_cols=60  Identities=15%  Similarity=0.387  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc-cCCCCCCC
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM-SAPSGFLP   83 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~-~~~p~f~p   83 (136)
                      +.|+.-++.+..+...++..+..|+.+...|.....+-|+|.||.+..|+++ ++.|-||-
T Consensus       165 ~~l~~ai~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~vRPAfmd  225 (267)
T PF10234_consen  165 KALKEAIKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERNQKRLQSLQSVRPAFMD  225 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHH
Confidence            3344445555555555566666666666666666667777777777778876 45676664

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 [].

>TIGR00219 mreC rod shape-determining protein MreC

Probab=93.23  E-value=0.39  Score=40.33  Aligned_cols=32  Identities=19%  Similarity=0.365  Sum_probs=15.0

Q ss_pred             HHHHhhHHHHHHHHHHHHHHH----HHHHHHHHhHH
Q 032660           32 KLKQSTEDLQEKIKELKAEKN----ELRDEKQRLKA   63 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKn----ELrdEk~~Lk~   63 (136)
                      .|++||+.|++++..|..+.+    ||+.||.+|+.
T Consensus        70 ~l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~  105 (283)
T TIGR00219        70 NLEYENYKLRQELLKKNQQLEILTQNLKQENVRLRE  105 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555444433322    35555555544

MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.

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

Probab=93.21  E-value=0.81  Score=40.00  Aligned_cols=45  Identities=16%  Similarity=0.311  Sum_probs=29.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      +++-++..+.+|..+++.|..+|+.|+++.+.+..+..++-.+|.
T Consensus       131 l~d~~l~~~~~l~~~~~~L~~enerL~~e~~~~~~qlE~~v~~K~  175 (342)
T PF06632_consen  131 LFDWCLDANSRLQAENEHLQKENERLESEANKLLKQLEKFVNAKE  175 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566667777777777777777777766666555555555554

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.

>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=93.16  E-value=1.2  Score=36.21  Aligned_cols=44  Identities=23%  Similarity=0.314  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      |..++..|+.+.+.|+..++.++..-+.++.+...|+.+++.++
T Consensus        54 L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~~~~   97 (251)
T PF11932_consen   54 LLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIEQIE   97 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444444444444444444444443

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.

>PRK05771 V-type ATP synthase subunit I; Validated

Probab=93.15  E-value=0.36  Score=44.17  Aligned_cols=62  Identities=23%  Similarity=0.416  Sum_probs=29.7

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHH------------hhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           13 ATILSDVVRMMEQLRTEAQKLKQ------------STEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        13 AsIL~DAir~lkqLr~e~~~Lk~------------~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+-+.++++.|++...+.+.+..            -.....++..++..|-++|.+++..|+++++++++++..
T Consensus        52 ~~~~~~~l~~L~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~i~~l~~~~~~L~~~~~~l~~~~~~  125 (646)
T PRK05771         52 LTKLSEALDKLRSYLPKLNPLREEKKKVSVKSLEELIKDVEEELEKIEKEIKELEEEISELENEIKELEQEIER  125 (646)
T ss_pred             HHHHHHHHHHHHHhccccccchhhhccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34456667777666555332111            011223344444455555555555555555555555444

>TIGR02209 ftsL_broad cell division protein FtsL

Probab=93.06  E-value=0.87  Score=30.77  Aligned_cols=36  Identities=33%  Similarity=0.442  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRD   56 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrd   56 (136)
                      .-+.+++.++++++.+++.++++...|+.|.+.|.+
T Consensus        24 ~~~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~   59 (85)
T TIGR02209        24 HQTRQLNNELQKLQLEIDKLQKEWRDLQLEVAELSR   59 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            345577777777777777777777777777777765

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.

>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=93.04  E-value=0.79  Score=35.68  Aligned_cols=31  Identities=35%  Similarity=0.482  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           40 LQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        40 L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      +.+|++.|+.|-.+...|...||.+.++|+.
T Consensus       159 ~~~ei~~lk~el~~~~~~~~~LkkQ~~~l~~  189 (192)
T PF05529_consen  159 LSEEIEKLKKELEKKEKEIEALKKQSEGLQK  189 (192)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3344444444444444444444444444443

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

>smart00787 Spc7 Spc7 kinetochore protein

Probab=93.02  E-value=0.68  Score=39.75  Aligned_cols=52  Identities=23%  Similarity=0.351  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +++||.++.++..+++....++.++..+.+++++.....+.+|..++.++..
T Consensus       206 L~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I~~  257 (312)
T smart00787      206 LDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIAE  257 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444555555555555555555555555555544444444444444444444

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

>PF14282 FlxA: FlxA-like protein

Probab=92.99  E-value=0.38  Score=35.12  Aligned_cols=53  Identities=21%  Similarity=0.342  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHH----HHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEK----IKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee----~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      ...+++|..+++.|.+.+..|.+.    .+.-+.....|..+...|.++|-.|+.+.
T Consensus        18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~   74 (106)
T PF14282_consen   18 DSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQ   74 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456667777777777776666662    13333334444555555555555554443

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=92.94  E-value=0.41  Score=39.04  Aligned_cols=42  Identities=29%  Similarity=0.528  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      +.++-..+|++|.++||++|+.|+.+...+    ++|++|+.+|+.
T Consensus        66 ~~~~~~~~l~~en~~L~~e~~~l~~~~~~~----~~l~~en~~L~~  107 (276)
T PRK13922         66 ESLASLFDLREENEELKKELLELESRLQEL----EQLEAENARLRE  107 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHH
Confidence            344556666777777777777766666544    244455555544

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

Probab=92.90  E-value=1.2  Score=35.83  Aligned_cols=60  Identities=20%  Similarity=0.388  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |..+=+.+++.|..|+..+|..-........++..|-..|.+-...+..|.++|+.+++.
T Consensus        21 IT~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~   80 (201)
T PF13851_consen   21 ITLNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKN   80 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            556667778888888877777666666666666666666666666666666666666554

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

Probab=92.69  E-value=1.1  Score=34.89  Aligned_cols=27  Identities=22%  Similarity=0.487  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           47 LKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        47 L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +..||.+.|+|...++..+..++..+.
T Consensus       111 ~n~eK~~~r~e~~~~~~ki~e~~~ki~  137 (177)
T PF07798_consen  111 LNLEKGRIREEQAKQELKIQELNNKID  137 (177)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334566677776666666655554443

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=92.67  E-value=1.4  Score=30.36  Aligned_cols=53  Identities=26%  Similarity=0.442  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |++|-.++..|=..+..|+++...|..+-..++.|...|....+---+.+.+|
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            45666666666666666666666666666666666666666555555555554

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.

>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=92.59  E-value=1.5  Score=34.94  Aligned_cols=52  Identities=23%  Similarity=0.413  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      ...-+.+++.++.+++..+..|++++..++.+..++|++...++..++....
T Consensus        54 ~~~~~~~~~~~~~~~~~r~~~l~~~i~~~~~~i~~~r~~l~~~~~~l~~~~~  105 (302)
T PF10186_consen   54 QLLEIQQLKREIEELRERLERLRERIERLRKRIEQKRERLEELRESLEQRRS  105 (302)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3345556666666666666666666655555555555554444444444333

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

>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=92.58  E-value=1.8  Score=32.50  Aligned_cols=54  Identities=26%  Similarity=0.506  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      .|-+|.+|....++-....+.|.++++.+..+...|.-...+|+.+.+.++.++
T Consensus        36 vin~i~~Ll~~~~r~~~~~e~l~~~~~~l~~d~~~l~~~~~rL~~~~~~~ere~   89 (151)
T PF11559_consen   36 VINCIYDLLQQRDRDMEQREDLSDKLRRLRSDIERLQNDVERLKEQLEELEREL   89 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555555555555555555555555554444444443

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.

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=92.55  E-value=0.84  Score=41.85  Aligned_cols=60  Identities=8%  Similarity=0.158  Sum_probs=47.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           14 TILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        14 sIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +-|.+.=.-.++|..++++||.+.+.+.....++..+.++|.+|+..|+.+.+.+-.+.-
T Consensus        69 SALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~~~~  128 (475)
T PRK13729         69 HATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGANPV  128 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcCCC
Confidence            346777778889999999998888877788888888888888999999888865555533

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

Probab=92.54  E-value=0.95  Score=33.26  Aligned_cols=41  Identities=27%  Similarity=0.483  Sum_probs=25.7

Q ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           32 KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      .|-.++..|+++++.+..+..+|+.+...++.++..|..++
T Consensus        77 ~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~  117 (118)
T PF13815_consen   77 YLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKES  117 (118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45555666666666666666666666666666666665554

>PRK05431 seryl-tRNA synthetase; Provisional

Probab=92.54  E-value=0.71  Score=40.78  Aligned_cols=53  Identities=25%  Similarity=0.356  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHH---HHHHHHHHHhHHHHHHHHHHHHh
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEK---NELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EK---nELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      -.++|+.+++.|+.+...+..+++.++..+   .+|.+|-..|+.++..|+.+++.
T Consensus        36 ~~r~l~~~~~~lr~~rn~~sk~i~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~   91 (425)
T PRK05431         36 ERRELQTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKELKEEIKALEAELDE   91 (425)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346677777888887777777776533322   13444444444444444444433

>PHA03011 hypothetical protein; Provisional

Probab=92.45  E-value=1.4  Score=33.57  Aligned_cols=59  Identities=19%  Similarity=0.382  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +..-+..|..|+.+-+.|-++...+..+++.+..=..+--||---|++|++||..++--
T Consensus        59 ~Nai~e~ldeL~~qYN~L~dEYn~i~Ne~k~~~~iIQdn~d~I~~LraeIDkLK~niaN  117 (120)
T PHA03011         59 INAIIEILDELIAQYNELLDEYNLIENEIKDLEIIIQDNDDEIHFLRAEIDKLKENIAN  117 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHhc
Confidence            44567889999999999999999999999999988888888999999999999888754

>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=92.34  E-value=1.7  Score=32.54  Aligned_cols=47  Identities=26%  Similarity=0.536  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      +..|++++.+|+..++.|++++.++..|...+..+-..|+.++..++
T Consensus        61 ~~~l~~d~~~l~~~~~rL~~~~~~~ere~~~~~~~~~~l~~~~~~~~  107 (151)
T PF11559_consen   61 LRRLRSDIERLQNDVERLKEQLEELERELASAEEKERQLQKQLKSLE  107 (151)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555555555555555554444444444333333333333333

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.

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

Probab=92.33  E-value=1.6  Score=29.55  Aligned_cols=46  Identities=20%  Similarity=0.453  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      |.+|-++++.|......|.+++..|+.+-....+|-.+-..-++++
T Consensus         5 id~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN~   50 (56)
T PF04728_consen    5 IDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDNI   50 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            5677777777777777777777777766665555555544444433

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.

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

Probab=92.21  E-value=1.1  Score=36.60  Aligned_cols=35  Identities=34%  Similarity=0.550  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           38 EDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      ..+.+++..++...+.|+.+...|++.+..|+.++
T Consensus       212 ~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l  246 (312)
T PF00038_consen  212 ESAKEELKELRRQIQSLQAELESLRAKNASLERQL  246 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHhHHHHHHhhhhHhhhhhhccccchhhhhhhH
Confidence            33333333444444444444344444444444333

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 ....

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=92.20  E-value=0.59  Score=40.34  Aligned_cols=49  Identities=24%  Similarity=0.535  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCCC
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS   79 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~~p   79 (136)
                      ..|+.+..+++..++.|++..++|..+++.       ++.++++++.+++.+..+|
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~   52 (389)
T PRK03992          4 EALEERNSELEEQIRQLELKLRDLEAENEK-------LERELERLKSELEKLKSPP   52 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHhhCCC
Confidence            345555555555555555555555555444       4455555555555555444

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

Probab=92.18  E-value=1  Score=31.83  Aligned_cols=58  Identities=29%  Similarity=0.532  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHH---HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQE---KIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~e---e~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ..+.-+.+||++-+.+.+++..+..   +..+|..|-.++.++...|+.+...++.++..+
T Consensus        40 ~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~~e~~l~~~  100 (108)
T PF02403_consen   40 ELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKELEEELNEL  100 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456677888888888887777765   578888888888888888888888888888874

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 ....

>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=92.16  E-value=1.7  Score=32.44  Aligned_cols=60  Identities=25%  Similarity=0.413  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccC
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA   77 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~   77 (136)
                      +-...+.+|+.+..+|.+.|-.++.++..++.+..++-++-..|+.+-..++++++.++.
T Consensus        31 ~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~~k~~~~~~l~~   90 (150)
T PF07200_consen   31 ELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQEKEQQQDELSS   90 (150)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            334445555666666666666666666777777777777777888888888888877643

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.

>smart00787 Spc7 Spc7 kinetochore protein

Probab=92.16  E-value=1.2  Score=38.35  Aligned_cols=49  Identities=22%  Similarity=0.395  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      =|+.+-.++...+...+.++++.+.++...++..++|+.+..+|..++.
T Consensus       212 ~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I~~ae~  260 (312)
T smart00787      212 KLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIAEAEK  260 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333334444444444444444444444444444444444444443333

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

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

Probab=92.15  E-value=0.79  Score=42.88  Aligned_cols=56  Identities=23%  Similarity=0.357  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      .|..+|..+...++..+..|.++++.|+.||+........|+..+.+|.+|+....
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            58899999999999999999999999999999999999999999999999888743

>TIGR00219 mreC rod shape-determining protein MreC

Probab=92.10  E-value=1.3  Score=37.33  Aligned_cols=22  Identities=14%  Similarity=0.157  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 032660           38 EDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      ..|.+|.+.|+.|..+|+.+.+
T Consensus        69 ~~l~~EN~~Lr~e~~~l~~~~~   90 (283)
T TIGR00219        69 NNLEYENYKLRQELLKKNQQLE   90 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555444433333

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.

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

Probab=91.99  E-value=1.1  Score=33.37  Aligned_cols=53  Identities=28%  Similarity=0.417  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +++++..++.|..+|..|-+.+-++..+-+++|++-..+..+...|+.++...
T Consensus        29 ~~~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~~k   81 (150)
T PF07200_consen   29 VQELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQEK   81 (150)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77888888888999999988888888888888888888888888888887764

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.

>TIGR01554 major_cap_HK97 phage major capsid protein, HK97 family

Probab=91.89  E-value=0.82  Score=38.84  Aligned_cols=19  Identities=11%  Similarity=0.335  Sum_probs=11.1

Q ss_pred             HHHHHHHHHHHHhhHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQE   42 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~e   42 (136)
                      ++||.+.+.++.+..+|.+
T Consensus         2 ~el~~~~~~~~~~~r~l~~   20 (378)
T TIGR01554         2 SELKEQREEIVAEIRSLLD   20 (378)
T ss_pred             hhHHHHHHHHHHHHHHHHh
Confidence            4566666666665555554

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.

>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=91.86  E-value=0.57  Score=30.05  Aligned_cols=30  Identities=30%  Similarity=0.574  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           41 QEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        41 ~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      .....+|..+..+|..|+..|+.++..|+.
T Consensus        24 k~~~~~le~~~~~L~~en~~L~~~i~~L~~   53 (54)
T PF07716_consen   24 KQREEELEQEVQELEEENEQLRQEIAQLER   53 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            344455555555555666666666665554

; 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 ....

>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]

Probab=91.83  E-value=1.1  Score=41.91  Aligned_cols=49  Identities=31%  Similarity=0.367  Sum_probs=31.9

Q ss_pred             CchhhhHHHHH----HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 032660           10 TDKATILSDVV----RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEK   58 (136)
Q Consensus        10 ~DKAsIL~DAi----r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk   58 (136)
                      |+|+.|+.+-+    .=+.++..|.-+|-..+.+++++++++..|||||-+=.
T Consensus       211 N~q~~s~~eel~~kt~el~~q~Ee~skLlsql~d~qkk~k~~~~Ekeel~~~L  263 (596)
T KOG4360|consen  211 NTQARSGQEELQSKTKELSRQQEENSKLLSQLVDLQKKIKYLRHEKEELDEHL  263 (596)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence            56666664433    23445566666777777777788888888888775433

>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=91.82  E-value=2  Score=34.19  Aligned_cols=15  Identities=27%  Similarity=0.499  Sum_probs=5.5

Q ss_pred             HHHHHHHHHHhhHHH
Q 032660           26 LRTEAQKLKQSTEDL   40 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L   40 (136)
                      |+.++++++++++..
T Consensus        75 l~~~i~~~~~~i~~~   89 (302)
T PF10186_consen   75 LRERIERLRKRIEQK   89 (302)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            333333333333333

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

>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=91.81  E-value=2.4  Score=28.86  Aligned_cols=51  Identities=27%  Similarity=0.452  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      =||-=..+..|+.+.|..|-.++...++-...-.+|..|...|+.+++.+.
T Consensus         9 EirakQ~~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee~r   59 (61)
T PF08826_consen    9 EIRAKQAIQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEMEELR   59 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            355556678888888888888888888888777777777777777777654

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=91.76  E-value=1.8  Score=36.91  Aligned_cols=15  Identities=27%  Similarity=0.248  Sum_probs=6.1

Q ss_pred             HhHHHHHHHHHHHHh
Q 032660           60 RLKADKEKLEQQVKA   74 (136)
Q Consensus        60 ~Lk~eke~Le~qlk~   74 (136)
                      .|+.+++...++|..
T Consensus       117 sl~~q~~~~~~~L~~  131 (314)
T PF04111_consen  117 SLKNQYEYASNQLDR  131 (314)
T ss_dssp             HHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHH
Confidence            344444444444433

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.

>PRK09039 hypothetical protein; Validated

Probab=91.72  E-value=1.6  Score=37.73  Aligned_cols=54  Identities=13%  Similarity=0.232  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ....+.+.++..|+.+++.|+..+..|..+.++++++....+..++.|+..|..
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            344455666778888888888888888888888888888888888888877766

>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 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

Probab=91.70  E-value=0.19  Score=34.74  Aligned_cols=49  Identities=22%  Similarity=0.364  Sum_probs=30.6

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 032660           10 TDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEK   58 (136)
Q Consensus        10 ~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk   58 (136)
                      -|++-|..|.-.++..|..+++.++++...|....+++..+.+++++..
T Consensus        51 vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l   99 (106)
T PF01920_consen   51 VGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKL   99 (106)
T ss_dssp             ETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555666666666666666666666666666666666655543

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 beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. 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: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.

>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=91.66  E-value=1.4  Score=41.05  Aligned_cols=8  Identities=25%  Similarity=0.580  Sum_probs=2.9

Q ss_pred             HHHHHhhH
Q 032660           31 QKLKQSTE   38 (136)
Q Consensus        31 ~~Lk~~n~   38 (136)
                      ..|+.++.
T Consensus       160 ~~Le~e~~  167 (546)
T PF07888_consen  160 EQLEEEVE  167 (546)
T ss_pred             HHHHHHHH
Confidence            33333333

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 [].

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

Probab=91.58  E-value=0.66  Score=41.82  Aligned_cols=51  Identities=27%  Similarity=0.419  Sum_probs=37.3

Q ss_pred             CCchhhhHHHHHHHHHHHHHHHHH---HHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 032660            9 KTDKATILSDVVRMMEQLRTEAQK---LKQSTEDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus         9 K~DKAsIL~DAir~lkqLr~e~~~---Lk~~n~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      |.+|.+||.-++.|+..|+..-++   +......|+..++.|...+.||..+..
T Consensus       268 ~~nKgtILk~s~dYIr~Lqq~~q~~~E~~~rqk~le~~n~~L~~rieeLk~~~~  321 (411)
T KOG1318|consen  268 KSNKGTILKASCDYIRELQQTLQRARELENRQKKLESTNQELALRIEELKSEAG  321 (411)
T ss_pred             hcccchhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHhHHHHHHHHHHHHHHHHH
Confidence            556999998888888888776664   444556677777777777777776655

>PRK11415 hypothetical protein; Provisional

Probab=91.56  E-value=1.1  Score=30.90  Aligned_cols=54  Identities=19%  Similarity=0.262  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH--------HHHHHHHHHHHhHHHHHHHHH
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKA--------EKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~--------EKnELrdEk~~Lk~eke~Le~   70 (136)
                      .|.|.-|++=-....+|.+++..|..+|+.+..        +..+|+-+|.+||.+|.++=.
T Consensus         6 ~d~I~~Lk~~D~~F~~L~~~h~~Ld~~I~~lE~~~~~~~d~~i~~LKk~KL~LKDeI~~~L~   67 (74)
T PRK11415          6 RDLISRLKNENPRFMSLFDKHNKLDHEIARKEGSDGRGYNAEVVRMKKQKLQLKDEMLKILQ   67 (74)
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHHHHHHHH
Confidence            356666766667777777777777777765543        566677777777766665543

>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea

Probab=91.54  E-value=1.1  Score=32.01  Aligned_cols=49  Identities=10%  Similarity=0.239  Sum_probs=26.3

Q ss_pred             CCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660            9 KTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus         9 K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      ..|.+-|..|--.++..|..+++.+..+...|..+++++..+.++|+.+
T Consensus        51 ~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk~~   99 (105)
T cd00632          51 LVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQEK   99 (105)
T ss_pred             HhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555555555555555555555555555444443

Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=91.48  E-value=0.86  Score=39.32  Aligned_cols=44  Identities=23%  Similarity=0.361  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      ...++.|+.+++.|+..+..|..+.+.++.+..+|+++...|+.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   50 (389)
T PRK03992          7 EERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKS   50 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            34567788999999999999999999999999999998877765

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=91.44  E-value=0.96  Score=33.11  Aligned_cols=34  Identities=12%  Similarity=0.250  Sum_probs=23.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           37 TEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        37 n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      +..++.++.+++.|..+|++++..|+.|+++|++
T Consensus        29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~   62 (105)
T PRK00888         29 YWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG   62 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            4555666666666666667777777777777765

>TIGR02231 conserved hypothetical protein

Probab=91.35  E-value=1.6  Score=38.93  Aligned_cols=66  Identities=18%  Similarity=0.321  Sum_probs=44.7

Q ss_pred             chhhhHHHHHHHHHHHHH---------------HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           11 DKATILSDVVRMMEQLRT---------------EAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        11 DKAsIL~DAir~lkqLr~---------------e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |+.+.+-.-+.+|..++.               .+.++.+-.....+++.++..++.+|..+...|+.++++|+++|..+
T Consensus        92 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l  171 (525)
T TIGR02231        92 DRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTEDREAERRIRELEKQLSELQNELNAL  171 (525)
T ss_pred             HHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            344555555666666653               23456666666666777777777888888888888888888887775


Q ss_pred             c
Q 032660           76 S   76 (136)
Q Consensus        76 ~   76 (136)
                      +
T Consensus       172 ~  172 (525)
T TIGR02231       172 L  172 (525)
T ss_pred             c
Confidence            4

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.

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

Probab=91.34  E-value=1.5  Score=34.96  Aligned_cols=25  Identities=32%  Similarity=0.676  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELK   48 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~   48 (136)
                      .+|..++..|+.++..|+.++.+|+
T Consensus       123 ~~l~~~i~~L~~e~~~L~~~~~~l~  147 (189)
T PF10211_consen  123 QELEEEIEELEEEKEELEKQVQELK  147 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444555555555444444443

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 [].

>KOG4797 consensus Transcriptional regulator [Transcription]

Probab=91.25  E-value=0.78  Score=35.23  Aligned_cols=33  Identities=30%  Similarity=0.441  Sum_probs=23.7

Q ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 032660           34 KQSTEDLQEKIKELKAEKNELRDEKQRLKADKE   66 (136)
Q Consensus        34 k~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke   66 (136)
                      ++|.+.|.+.|++|...-+.|+.||.-||+-..
T Consensus        66 REEVe~Lk~qI~eL~er~~~Le~EN~lLk~~~s   98 (123)
T KOG4797|consen   66 REEVEVLKEQIRELEERNSALERENSLLKTLAS   98 (123)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            455666667777777777788888888886543

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

Probab=91.23  E-value=1.2  Score=36.81  Aligned_cols=58  Identities=22%  Similarity=0.433  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .++-....+|+.+..+..++...|..++.++..+...|++++..-..|.++|+.++..
T Consensus        57 ~eaee~~~rL~~~~~~~~eEk~~Le~e~~e~~~~i~~l~ee~~~ke~Ea~~lq~el~~  114 (246)
T PF00769_consen   57 QEAEEEKQRLEEEAEMQEEEKEQLEQELREAEAEIARLEEESERKEEEAEELQEELEE  114 (246)
T ss_dssp             HHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566677778888888888888888888888888888888888888888888887766

Ezrin was first identified as a constituent of microvilli [], radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions [], and moesin as a heparin binding protein []. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain; an extended alpha-helical domain; and a charged C-terminal domain []. Ezrin, radixin and merlin also contain a polyproline region between the helical and C-terminal domains. The N-terminal domain is highly conserved, and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily. ERM proteins crosslink actin filaments with plasma membranes. They co-localise with CD44 at actin filament-plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains [].; GO: 0008092 cytoskeletal protein binding, 0005737 cytoplasm, 0019898 extrinsic to membrane; PDB: 2I1J_A 2I1K_A 1E5W_A 1EF1_C.

>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=91.15  E-value=2.4  Score=30.91  Aligned_cols=57  Identities=21%  Similarity=0.424  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+..+-|.+++.+.-+++..|..|-.++.+|+.+..+-++ ...+..++++++.+++.
T Consensus        13 ~~l~~~L~~v~~~~l~l~~~n~el~~el~~l~~~~~~~~~-~~~~~~~l~~~~~~lk~   69 (106)
T PF05837_consen   13 RSLQEKLSDVEKKRLRLKRRNQELAQELLELAEKQKSQRE-DEELSEKLEKLEKELKK   69 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcc-chHHHHHHHHHHHHHHH
Confidence            3444445555555555555555555556555555554444 44566788888887776

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

>TIGR00414 serS seryl-tRNA synthetase

Probab=91.08  E-value=1.6  Score=38.55  Aligned_cols=52  Identities=25%  Similarity=0.424  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHH----HHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAE----KNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~E----KnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .++|+.|++.|+.+...+..+++.++..    ..+|+++-..|+.++..|+.+++.
T Consensus        39 ~r~~~~~~~~l~~erN~~sk~i~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~   94 (418)
T TIGR00414        39 RKKLLSEIEELQAKRNELSKQIGKAKGQKKDKIEEIKKELKELKEELTELSAALKA   94 (418)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567778888888888888777664322    346666666666666666666555

This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.

>PF14282 FlxA: FlxA-like protein

Probab=90.94  E-value=1.6  Score=31.85  Aligned_cols=49  Identities=22%  Similarity=0.464  Sum_probs=37.0

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHH----HHHHHHHHhHHHHHHHHHHHHhc
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKN----ELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKn----ELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      -.+|+.|+..+..|++++++|...++    +-+.....|..+|.-|+.||..+
T Consensus        18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~ql   70 (106)
T PF14282_consen   18 DSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQL   70 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46788888888888888888887433    33444557888888888888875

>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=90.94  E-value=1.5  Score=34.12  Aligned_cols=47  Identities=28%  Similarity=0.513  Sum_probs=23.1

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +.++..|+++...+..+.+.|..|..-||.||-.|..+-.+.+.++.
T Consensus        51 k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv~   97 (140)
T PF10473_consen   51 KAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKKQEKVS   97 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44445555555555555555555555555555544444444444433

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

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

Probab=90.93  E-value=1.1  Score=38.86  Aligned_cols=54  Identities=24%  Similarity=0.516  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      ..=|+.++.+++.|++....+.+++++|+.++|++.+.-+.|-.+..++-....
T Consensus        47 n~kvrE~~e~~~elr~~rdeineev~elK~kR~ein~kl~eL~~~~~~l~e~~~  100 (294)
T COG1340          47 NAKVRELREKAQELREERDEINEEVQELKEKRDEINAKLQELRKEYRELKEKRN  100 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            344566677777777777777777777777777776666665555555544433

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

Probab=90.92  E-value=1  Score=37.53  Aligned_cols=37  Identities=35%  Similarity=0.519  Sum_probs=14.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           36 STEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        36 ~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +.++++++...|+..-.++.+|-.+|..|-.+|+.|+
T Consensus       173 ~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i  209 (216)
T KOG1962|consen  173 KLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQI  209 (216)
T ss_pred             HHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333344444444444443

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=90.75  E-value=1.8  Score=41.25  Aligned_cols=48  Identities=27%  Similarity=0.506  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      ++|.+|..+-.++++..+.+++..++++..+++|++++..|+.+++++
T Consensus       520 ~li~~l~~~~~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~  567 (782)
T PRK00409        520 ELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKL  567 (782)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555555555555555555555555444433

>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=90.75  E-value=2.2  Score=31.81  Aligned_cols=49  Identities=24%  Similarity=0.432  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHH----HHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKI----KELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~----~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      +.+++.++..|+.+..+.....    .....+|..|..|+..++.-++.|..|
T Consensus        68 ~~~~~~~~~~l~~~~~~a~~~l~~~e~sw~~qk~~le~e~~~~~~r~~dL~~Q  120 (132)
T PF07926_consen   68 LQELQQEINELKAEAESAKAELEESEASWEEQKEQLEKELSELEQRIEDLNEQ  120 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344455555544443333332    234445555555555555555555443

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

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

Probab=90.70  E-value=1.8  Score=39.21  Aligned_cols=51  Identities=22%  Similarity=0.285  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      -..+|..++++|+.++.++..++.+...+.++++.....+...++.|+.|-
T Consensus        60 ~~~kL~~~lk~~e~~i~~~~~ql~~s~~~l~~~~~~I~~~~~~l~~l~~q~  110 (420)
T COG4942          60 QRAKLEKQLKSLETEIASLEAQLIETADDLKKLRKQIADLNARLNALEVQE  110 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHHHHHHH
Confidence            344555555566666666666665555666666666666666666666554

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=90.65  E-value=1.2  Score=42.28  Aligned_cols=44  Identities=20%  Similarity=0.431  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      ++.-.+-++.|+..+++|+.+|..|+.++.+++.|..+|+++..
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            34445556667777777777777777777666666666655544

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

Probab=90.60  E-value=1.6  Score=31.77  Aligned_cols=27  Identities=30%  Similarity=0.432  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           43 KIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        43 e~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      +.+.|..+..|++-+-..+.+.+.-++
T Consensus        66 dv~~L~l~l~el~G~~~~l~~~l~~v~   92 (106)
T PF10805_consen   66 DVHDLQLELAELRGELKELSARLQGVS   92 (106)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            333333333333333333333333333

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

>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=90.58  E-value=0.43  Score=32.70  Aligned_cols=28  Identities=36%  Similarity=0.533  Sum_probs=14.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           36 STEDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        36 ~n~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      +.+.|.+.|.+|...-++|+.||+.||+
T Consensus        15 EVevLK~~I~eL~~~n~~Le~EN~~Lk~   42 (59)
T PF01166_consen   15 EVEVLKEQIAELEERNSQLEEENNLLKQ   42 (59)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3344444444444445555566666654

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.

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

Probab=90.52  E-value=2  Score=32.91  Aligned_cols=27  Identities=33%  Similarity=0.545  Sum_probs=13.7

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           48 KAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        48 ~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ..|.+.|...+..|..++++++.+|+.
T Consensus        34 E~EI~sL~~K~~~lE~eld~~~~~l~~   60 (143)
T PF12718_consen   34 EQEITSLQKKNQQLEEELDKLEEQLKE   60 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333334444555555555555555554

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 [].

>PF14988 DUF4515: Domain of unknown function (DUF4515)

Probab=90.49  E-value=2.4  Score=34.39  Aligned_cols=50  Identities=22%  Similarity=0.401  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      ++.|..-...+..+|..|+.++.+|..|-..|++.+..|+..+..|.++-
T Consensus       151 ~~~l~e~~~~i~~EN~~L~k~L~~l~~e~~~L~~~~~~Le~qk~~L~~eq  200 (206)
T PF14988_consen  151 KKSLDEFTRSIKRENQQLRKELLQLIQEAQKLEARKSQLEKQKQQLQQEQ  200 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455566677888888888888888888888888888888888777663

>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=90.48  E-value=2.6  Score=31.87  Aligned_cols=31  Identities=32%  Similarity=0.468  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRD   56 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrd   56 (136)
                      |++-.+.|+.++.++...+.+|.++.+|++.
T Consensus        42 L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~   72 (107)
T PF09304_consen   42 LRNALQSLQAQNASRNQRIAELQAKIDEARR   72 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444444444444443

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.

>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=90.41  E-value=0.37  Score=34.30  Aligned_cols=24  Identities=33%  Similarity=0.603  Sum_probs=17.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           52 NELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        52 nELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +||++|+.+||.++.+|+.+|+.+
T Consensus         3 ~ei~eEn~~Lk~eiqkle~ELq~~   26 (76)
T PF07334_consen    3 HEIQEENARLKEEIQKLEAELQQN   26 (76)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            466777777777777777777664

This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.

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

Probab=90.41  E-value=3.9  Score=31.31  Aligned_cols=27  Identities=22%  Similarity=0.555  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELK   48 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~   48 (136)
                      .+++...+++.++..+..+.++++++.
T Consensus       124 ~~~~~~~~l~~l~~~~~~~~~e~~~l~  150 (191)
T PF04156_consen  124 LLKSVEERLDSLDESIKELEKEIRELQ  150 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555555555

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 [].

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=90.39  E-value=1.3  Score=42.02  Aligned_cols=60  Identities=25%  Similarity=0.432  Sum_probs=40.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH----------HHhHHHHHHHHHHHH
Q 032660           14 TILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEK----------QRLKADKEKLEQQVK   73 (136)
Q Consensus        14 sIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk----------~~Lk~eke~Le~qlk   73 (136)
                      .-+.+--+.|+.|+.|++.|+.+++.|+.++..|+.+..+++.+-          ..+..+|++|+..|+
T Consensus       422 ~~i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r~~~~~~~~~rei~~~~~~I~~L~~~L~  491 (652)
T COG2433         422 KRIKKLEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELE  491 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence            345555677888888888888888888888888888777776542          235555555555443

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

Probab=90.38  E-value=1.4  Score=40.95  Aligned_cols=35  Identities=31%  Similarity=0.515  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           41 QEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        41 ~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +.++..++..++-|.||+.+||.|..+|..+|+.+
T Consensus       154 eAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~  188 (546)
T KOG0977|consen  154 EAEINTLKRRIKALEDELKRLKAENSRLREELARA  188 (546)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH
Confidence            33456666777777777777777777777777664

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

Probab=90.36  E-value=1.8  Score=28.99  Aligned_cols=56  Identities=11%  Similarity=0.373  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH-HHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELK-AEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~-~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +--+.|..+...+++..+-...++-|++.+- .+|+.+.......+++..+|+.+|+
T Consensus        22 ~r~~~i~~~e~~l~ea~~~l~qMe~E~~~~p~s~r~~~~~kl~~yr~~l~~lk~~l~   78 (79)
T PF05008_consen   22 QRKSLIREIERDLDEAEELLKQMELEVRSLPPSERNQYKSKLRSYRSELKKLKKELK   78 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4445666666667777777777777777665 7888888888888888888888876

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.

>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=90.28  E-value=1.9  Score=37.68  Aligned_cols=50  Identities=22%  Similarity=0.361  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      ++-.+-..+.+|.++|..|+.+...|+.|-|++..+.-.+-.+|+.+|.+
T Consensus       131 l~d~~l~~~~~l~~~~~~L~~enerL~~e~~~~~~qlE~~v~~K~~~E~~  180 (342)
T PF06632_consen  131 LFDWCLDANSRLQAENEHLQKENERLESEANKLLKQLEKFVNAKEEHEED  180 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444455555555555555555555555555555555555555555544

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.

>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function

Probab=90.13  E-value=2.3  Score=37.40  Aligned_cols=55  Identities=31%  Similarity=0.556  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHH--------------------HHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELK--------------------AEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~--------------------~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+-+++|+.++++++++.+.|+..+..++                    ..+.+|.++...|+.++..|+.+++.
T Consensus       333 ~~~~~~l~~~~~~~~~~l~~l~~~l~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~l~~~l~~  407 (451)
T PF03961_consen  333 KEKLEELEEELEELKEELEKLKKNLKKLKKLKKQGKLPPEKKEQLKKLKEKKKELKEELKELKEELKELKEELER  407 (451)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44456666666666666666655554444                    34445555555555555555555554

The proteins are in the region of 500-600 amino acid residues in length.

>PF14645 Chibby: Chibby family

Probab=89.99  E-value=1.4  Score=33.10  Aligned_cols=47  Identities=26%  Similarity=0.294  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      ...+.++|+++|..|+||+++|+.+..=|-|=.+.-.+|-.-+|.+|
T Consensus        69 ~~~~~~~l~~~n~~L~EENN~Lklk~elLlDMLtettae~~l~ek~l  115 (116)
T PF14645_consen   69 DGEENQRLRKENQQLEEENNLLKLKIELLLDMLTETTAEAHLLEKEL  115 (116)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34678889999999999999999998888888887777777777665

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

Probab=89.96  E-value=2  Score=42.98  Aligned_cols=54  Identities=28%  Similarity=0.553  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      +++|..|+++|...+.+|.+++++++.+-.+-++|+...+.+|..|...++..+
T Consensus       403 ~~~L~~evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~l~k~i~~~~  456 (1074)
T KOG0250|consen  403 LEQLKKEVEKLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQLRKKIENIS  456 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555555555555555555555555555555566666666666666666654

>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=89.93  E-value=2.6  Score=36.99  Aligned_cols=66  Identities=23%  Similarity=0.391  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHH--------------------HHHHHHHHHhccCC
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKAD--------------------KEKLEQQVKAMSAP   78 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~e--------------------ke~Le~qlk~~~~~   78 (136)
                      -++-.+.++.+..+.++.+..+.+.+.+++.|.|++-+|....|.+                    +-+|.++++.|++.
T Consensus       271 l~~eYr~~~~~ls~~~~~y~~~s~~V~~~t~~L~~IseeLe~vK~emeerg~~mtD~sPlv~IKqAl~kLk~EI~qMdvr  350 (359)
T PF10498_consen  271 LIQEYRSAQDELSEVQEKYKQASEGVSERTRELAEISEELEQVKQEMEERGSSMTDGSPLVKIKQALTKLKQEIKQMDVR  350 (359)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHhhhh
Confidence            3344444555555555555555555556666666555555444433                    34556666667666


Q ss_pred             CCCCCC
Q 032660           79 SGFLPH   84 (136)
Q Consensus        79 p~f~ph   84 (136)
                      -|++-|
T Consensus       351 IGVleh  356 (359)
T PF10498_consen  351 IGVLEH  356 (359)
T ss_pred             hheehh
Confidence            666554

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.

>PLN02678 seryl-tRNA synthetase

Probab=89.93  E-value=3.8  Score=36.97  Aligned_cols=52  Identities=25%  Similarity=0.374  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHH---HHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELK---AEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~---~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .++|+.+++.|+.+...+..++..++   .+..+|.+|-..|+.++..|+.+++.
T Consensus        42 ~r~l~~~~e~lr~erN~~sk~I~~~k~~~~~~~~l~~~~~~Lk~ei~~le~~~~~   96 (448)
T PLN02678         42 WRQRQFELDSLRKEFNKLNKEVAKLKIAKEDATELIAETKELKKEITEKEAEVQE   96 (448)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35566777777777777777665433   12234444444455555554444433

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

Probab=89.88  E-value=4.3  Score=32.61  Aligned_cols=43  Identities=26%  Similarity=0.434  Sum_probs=35.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      .|..+-.-++.+..++..|+-+++.|+.....|..|++||.+.
T Consensus        87 ~L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~~k  129 (201)
T PF13851_consen   87 SLQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQERDELYRK  129 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566667788888888889999999999999999998888754

>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=89.58  E-value=2.7  Score=36.76  Aligned_cols=43  Identities=28%  Similarity=0.394  Sum_probs=30.2

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 032660           13 ATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR   55 (136)
Q Consensus        13 AsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELr   55 (136)
                      +.+|+|+-.-.+.|..|+..|+.....++.+++.|..-.+..|
T Consensus        71 a~lL~~sre~Nk~L~~Ev~~Lrqkl~E~qGD~KlLR~~la~~r  113 (319)
T PF09789_consen   71 AQLLSESREQNKKLKEEVEELRQKLNEAQGDIKLLREKLARQR  113 (319)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHhhh
Confidence            4667788777777777777777777777777766665444443

>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=89.49  E-value=0.2  Score=36.06  Aligned_cols=47  Identities=32%  Similarity=0.574  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADK   65 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~ek   65 (136)
                      -=.+|.+|..++..|..+|..|..+++.|..+-.+++++...|+..+
T Consensus        23 VD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~~~l   69 (131)
T PF05103_consen   23 VDDFLDELAEELERLQRENAELKEEIEELQAQLEELREEEESLQRAL   69 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT---------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHhh
Confidence            34678888888888888888888777777777777766666655544

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.

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

Probab=89.41  E-value=1.1  Score=32.73  Aligned_cols=43  Identities=28%  Similarity=0.469  Sum_probs=31.2

Q ss_pred             HHHHHHHhhHH-HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           29 EAQKLKQSTED-LQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        29 e~~~Lk~~n~~-L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      .|.-||.+++. .+..++.|..+++.|.+|+..|+.+++.-..+
T Consensus        35 KV~~LKksYe~rwek~v~~L~~e~~~l~~E~e~L~~~l~~e~~E   78 (87)
T PF12709_consen   35 KVKALKKSYEARWEKKVDELENENKALKRENEQLKKKLDTEREE   78 (87)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46677777754 67778888888888888888887766654443

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 [].

>PF05701 WEMBL: Weak chloroplast movement under blue light; InterPro: IPR008545 This family consists of several plant proteins of unknown function

Probab=89.39  E-value=2.8  Score=37.97  Aligned_cols=58  Identities=21%  Similarity=0.410  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .++-.-|.....++..|+...+.|+.++...+.|.+.|++.-....+.+.+|+.+|..
T Consensus       291 e~ak~~L~~~k~E~~~L~~~vesL~~ELe~~K~el~~lke~e~~a~~~v~~L~~eL~~  348 (522)
T PF05701_consen  291 EEAKKELEKAKEEASSLRASVESLRSELEKEKEELERLKEREKEASSEVSSLEAELNK  348 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhHHHHHHH
Confidence            3444445555566667777777777777777777777777665555555555555444

Several sequences in this family are described as being myosin heavy chain-like.

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=89.38  E-value=4.2  Score=27.97  Aligned_cols=42  Identities=21%  Similarity=0.495  Sum_probs=27.4

Q ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           28 TEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        28 ~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      .+...|..++......+...-.|.++|++|+..|+.|.+.+.
T Consensus        26 ~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~~r   67 (69)
T PF14197_consen   26 IENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEELR   67 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            344445555555555567777777788888888877766554

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

Probab=89.32  E-value=3  Score=29.05  Aligned_cols=38  Identities=26%  Similarity=0.397  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      .+.+...+..++..++.+...|..|.+.|+=|.+.|.+
T Consensus        33 ~~~~~~~~~~~l~~l~~~~~~l~~e~~~L~lE~~~l~~   70 (97)
T PF04999_consen   33 SRHQSRQLFYELQQLEKEIDQLQEENERLRLEIATLSS   70 (97)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            44445555555555555555555555555555555443

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

>PRK04325 hypothetical protein; Provisional

Probab=89.32  E-value=5.5  Score=27.54  Aligned_cols=53  Identities=17%  Similarity=0.179  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      ..+...+.+|....+-.+..|.+|...--+.+.+...|+.+...|-.+++.+.
T Consensus         5 ~~~e~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl~~~~   57 (74)
T PRK04325          5 QEMEDRITELEIQLAFQEDLIDGLNATVARQQQTLDLLQAQLRLLYQQMRDAN   57 (74)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34555677777777777777777777777777777777777777777777764

>COG3937 Uncharacterized conserved protein [Function unknown]

Probab=89.31  E-value=2.6  Score=31.88  Aligned_cols=56  Identities=23%  Similarity=0.424  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhH-HHHHHHHHHHHHH--------HHHHHHHHHhHHHHHHHHHHHH
Q 032660           18 DVVRMMEQLRTEAQKLKQSTE-DLQEKIKELKAEK--------NELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~-~L~ee~~~L~~EK--------nELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +|-++|.+|..|++.-+.+.+ +++..++.+...-        .+|+++..+|+.+...||++++
T Consensus        43 Eak~~vddl~~q~k~~~~e~e~K~~r~i~~ml~~~~~~r~~~~~~l~~rvd~Lerqv~~Lenk~k  107 (108)
T COG3937          43 EAKRFVDDLLRQAKEAQGELEEKIPRKIEEMLSDLEVARQSEMDELTERVDALERQVADLENKLK  107 (108)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHhhhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHHHHhc
Confidence            577899999888884443322 2333444444333        5788888888888888888776

>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function

Probab=89.30  E-value=3.3  Score=36.40  Aligned_cols=33  Identities=24%  Similarity=0.537  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRD   56 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrd   56 (136)
                      .+|+.+.++|+++...+++++.+++.....|..
T Consensus       330 ~~l~~~~~~l~~~~~~~~~~l~~l~~~l~~l~~  362 (451)
T PF03961_consen  330 PELKEKLEELEEELEELKEELEKLKKNLKKLKK  362 (451)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            567777788888888888888777777655554

The proteins are in the region of 500-600 amino acid residues in length.

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

Probab=89.19  E-value=2.8  Score=30.55  Aligned_cols=32  Identities=25%  Similarity=0.421  Sum_probs=14.0

Q ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 032660           28 TEAQKLKQSTEDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        28 ~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      .++.+|..++..|..++..|+.+.+--|+||.
T Consensus        49 k~v~~L~~e~~~l~~E~e~L~~~l~~e~~Ek~   80 (87)
T PF12709_consen   49 KKVDELENENKALKRENEQLKKKLDTEREEKQ   80 (87)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444443

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 [].

>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=89.14  E-value=1.7  Score=27.82  Aligned_cols=30  Identities=37%  Similarity=0.644  Sum_probs=15.7

Q ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           34 KQSTEDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        34 k~~n~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      |.....|+.++..|+.|...|+.+...|+.
T Consensus        24 k~~~~~le~~~~~L~~en~~L~~~i~~L~~   53 (54)
T PF07716_consen   24 KQREEELEQEVQELEEENEQLRQEIAQLER   53 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            344455555555555555555555555544

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

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

Probab=89.11  E-value=4  Score=27.16  Aligned_cols=22  Identities=27%  Similarity=0.502  Sum_probs=13.9

Q ss_pred             HHHHHHHhHHHHHHHHHHHHhc
Q 032660           54 LRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        54 LrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      -|+....++.++++|+..|..|
T Consensus        44 er~kl~~~~~~~~~l~~~l~~L   65 (66)
T PF10458_consen   44 EREKLEELEEELEKLEEALEQL   65 (66)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHHHHhc
Confidence            3445556777777777777654

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.

>TIGR01069 mutS2 MutS2 family protein

Probab=89.10  E-value=2.9  Score=39.80  Aligned_cols=10  Identities=10%  Similarity=0.225  Sum_probs=4.4

Q ss_pred             hHHHHHHHHH
Q 032660           15 ILSDVVRMME   24 (136)
Q Consensus        15 IL~DAir~lk   24 (136)
                      ||..|-+++.
T Consensus       498 ii~~A~~~~~  507 (771)
T TIGR01069       498 IIEQAKTFYG  507 (771)
T ss_pred             HHHHHHHHHH
Confidence            4444444443

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

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

Probab=89.10  E-value=3.6  Score=32.78  Aligned_cols=47  Identities=30%  Similarity=0.459  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHH------HHHHHHHHHHHHHHHHHHHhHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQ------EKIKELKAEKNELRDEKQRLKADKE   66 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~------ee~~~L~~EKnELrdEk~~Lk~eke   66 (136)
                      ..=+.+++.++..|+++++.+.      ++...+-.+.++|+.+...|+.+.+
T Consensus        75 ~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~  127 (188)
T PF03962_consen   75 QKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKELE  127 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444443      2234445555555555555555544

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

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

Probab=89.04  E-value=2.5  Score=31.22  Aligned_cols=38  Identities=24%  Similarity=0.297  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      +..+.+|..+++.++++++.|..+...|+.|-+.|+|+
T Consensus        49 ~~~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg   86 (117)
T COG2919          49 AADVLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG   86 (117)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            34445555555555555555555555555555555554

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

Probab=88.96  E-value=2.7  Score=33.80  Aligned_cols=19  Identities=37%  Similarity=0.548  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 032660           38 EDLQEKIKELKAEKNELRD   56 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrd   56 (136)
                      ..+.+++.+|+...-||++
T Consensus       127 ~~~e~~i~~Le~ki~el~~  145 (190)
T PF05266_consen  127 KELESEIKELEMKILELQR  145 (190)
T ss_pred             hhHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444

>COG5481 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]

Probab=88.89  E-value=3.3  Score=28.84  Aligned_cols=47  Identities=28%  Similarity=0.442  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHH------HHHHHHHHHHHhHHHHHHHHHHH
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKA------EKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~------EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +|-.+.+|+++++.+-..|+.+.+      ...-+...|..||.++-+||.|+
T Consensus         9 irl~~arLrqeH~D~DaaInAmi~~~cD~L~iqRmKkKKLAlKDki~~lED~i   61 (67)
T COG5481           9 IRLTLARLRQEHADFDAAINAMIATGCDALRIQRMKKKKLALKDKITKLEDQI   61 (67)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHhCCcHHHHHHHHHHHHhHHHHHHHHHHhh
Confidence            445555566666655555555432      23345567788888888998886

>PRK02119 hypothetical protein; Provisional

Probab=88.84  E-value=6  Score=27.34  Aligned_cols=53  Identities=13%  Similarity=0.176  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      ..+...+.+|....+-.+..+.+|...--+.+.+...|+.+...|-++++.+.
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            44556666666666666666777776666666666777777777777776654

>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=88.79  E-value=2.8  Score=32.60  Aligned_cols=10  Identities=40%  Similarity=0.551  Sum_probs=3.9

Q ss_pred             HhHHHHHHHH
Q 032660           60 RLKADKEKLE   69 (136)
Q Consensus        60 ~Lk~eke~Le   69 (136)
                      .|+++|+.|+
T Consensus        55 eLk~~i~~lq   64 (155)
T PF06810_consen   55 ELKKQIEELQ   64 (155)
T ss_pred             HHHHHHHHHH
Confidence            3333333333

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

>TIGR00606 rad50 rad50

Probab=88.56  E-value=2.9  Score=41.53  Aligned_cols=60  Identities=10%  Similarity=0.243  Sum_probs=31.2

Q ss_pred             HHHHHHHH------HHHHHHHHHHHHhhH-----HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           16 LSDVVRMM------EQLRTEAQKLKQSTE-----DLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        16 L~DAir~l------kqLr~e~~~Lk~~n~-----~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |.|-+.++      +++..++..|..++.     .++.+.++|..+.|+|.-+++.+..++.+|+.|+..+
T Consensus      1017 l~dnL~~~~~~~~l~el~~eI~~l~~~~~~~~~~~~~~e~~~l~~~~~~l~~~~a~l~g~~k~le~qi~~l 1087 (1311)
T TIGR00606      1017 LQDNLTLRKRENELKEVEEELKQHLKEMGQMQVLQMKQEHQKLEENIDLIKRNHVLALGRQKGYEKEIKHF 1087 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56667777      455555555554443     2334444444444444444444445555566655553

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

>PRK14153 heat shock protein GrpE; Provisional

Probab=88.53  E-value=1.6  Score=35.58  Aligned_cols=46  Identities=20%  Similarity=0.362  Sum_probs=34.3

Q ss_pred             HHHHHHHHh--hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           28 TEAQKLKQS--TEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        28 ~e~~~Lk~~--n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      .+++.||++  +..+.+++..|+.+..+|++...++.+|.+++....+
T Consensus        24 ~~~~~~~~~~~~~~~~~ei~~l~~e~~elkd~~lR~~AEfeN~rKR~~   71 (194)
T PRK14153         24 EEAEELKEEPEDSTADSETEKCREEIESLKEQLFRLAAEFDNFRKRTA   71 (194)
T ss_pred             HHHHHHhhhhhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356677764  4577778888888888888888888888887765433

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

Probab=88.53  E-value=2  Score=28.98  Aligned_cols=35  Identities=23%  Similarity=0.500  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           40 LQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        40 L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |+.++..++..-+-+|.|++.++.+++++++-++.
T Consensus         5 lEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~   39 (55)
T PF05377_consen    5 LENELPRIESSINTVKKENEEISESVEKIEENVKD   39 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444455555555555555666555554

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) [].

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

Probab=88.40  E-value=2.9  Score=34.50  Aligned_cols=33  Identities=27%  Similarity=0.469  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR   55 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELr   55 (136)
                      ...|-.+.+.+..+-..|+.+..++..++..|+
T Consensus        35 a~~Leek~k~aeeea~~Le~k~~eaee~~~rL~   67 (246)
T PF00769_consen   35 AEELEEKLKQAEEEAEELEQKRQEAEEEKQRLE   67 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333333333333

Ezrin was first identified as a constituent of microvilli [], radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions [], and moesin as a heparin binding protein []. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain; an extended alpha-helical domain; and a charged C-terminal domain []. Ezrin, radixin and merlin also contain a polyproline region between the helical and C-terminal domains. The N-terminal domain is highly conserved, and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily. ERM proteins crosslink actin filaments with plasma membranes. They co-localise with CD44 at actin filament-plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains [].; GO: 0008092 cytoskeletal protein binding, 0005737 cytoplasm, 0019898 extrinsic to membrane; PDB: 2I1J_A 2I1K_A 1E5W_A 1EF1_C.

>PF08961 DUF1875: Domain of unknown function (DUF1875); InterPro: IPR015056 MIT can be found in the Nuclear receptor-binding factor 2, it has no known function

Probab=88.21  E-value=0.15  Score=43.13  Aligned_cols=11  Identities=27%  Similarity=0.501  Sum_probs=0.0

Q ss_pred             cccccCCCCCc
Q 032660          102 KLVPFIGYPGV  112 (136)
Q Consensus       102 k~~p~~~ypg~  112 (136)
                      |=+|++..|..
T Consensus       210 kdipip~lppl  220 (243)
T PF08961_consen  210 KDIPIPNLPPL  220 (243)
T ss_dssp             -----------
T ss_pred             ccCcCCCCCCC
Confidence            33677766543

; PDB: 2CRB_A.

>KOG2751 consensus Beclin-like protein [Signal transduction mechanisms]

Probab=88.19  E-value=2.2  Score=38.98  Aligned_cols=47  Identities=32%  Similarity=0.478  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      .++|..|.+.|+.++..|...+++|..|-.+|-.+...++.+++++.
T Consensus       178 ~~~~~~e~~~l~~eE~~L~q~lk~le~~~~~l~~~l~e~~~~~~~~~  224 (447)
T KOG2751|consen  178 EEDLLKELKNLKEEEERLLQQLEELEKEEAELDHQLKELEFKAERLN  224 (447)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45677777777777777777776666665555555555555544444

>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=88.18  E-value=6.7  Score=27.08  Aligned_cols=53  Identities=32%  Similarity=0.475  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      =-..|..+-.++...+..|+..++++..+.++|......+..+++.|+..++.
T Consensus        20 EGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l~~~l~~   72 (74)
T PF12329_consen   20 EGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESLEERLKR   72 (74)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            33566667777777777777777777777777777777778888887776654

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.

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=88.18  E-value=1.2  Score=37.53  Aligned_cols=40  Identities=25%  Similarity=0.503  Sum_probs=18.3

Q ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCCC
Q 032660           33 LKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS   79 (136)
Q Consensus        33 Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~~p   79 (136)
                      |+..++.|++..+++..|.+       .++.|+++++.+++.+..+|
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~   43 (364)
T TIGR01242         4 LDVRIRKLEDEKRSLEKEKI-------RLERELERLRSEIERLRSPP   43 (364)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHhCCC
Confidence            33344444444444444444       44444444555555544443

Many proteins may score above the trusted cutoff because an internal

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=88.13  E-value=3.2  Score=34.46  Aligned_cols=53  Identities=13%  Similarity=0.269  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      -+.+-||..+++.|+.++..|+-.+.++.-+.+.+.++-..|-.+++++-.++
T Consensus        53 ~~~~~~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~dld~r~~~~  105 (263)
T PRK10803         53 SQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDSLSSGG  105 (263)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            34566888888888888888888888888888888888888888888776544

>TIGR01069 mutS2 MutS2 family protein

Probab=88.11  E-value=3.9  Score=38.98  Aligned_cols=48  Identities=29%  Similarity=0.420  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEK   67 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~   67 (136)
                      -+++.+|..+..++.+....++...++++.++++|+++...|+.++++
T Consensus       514 ~~li~~L~~~~~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~  561 (771)
T TIGR01069       514 NVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERN  561 (771)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555444444444444444444445555555544444444443

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.

>PRK03918 chromosome segregation protein; Provisional

Probab=88.09  E-value=4.2  Score=37.72  Aligned_cols=30  Identities=27%  Similarity=0.418  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           45 KELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        45 ~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ..+..+.++++.+...|+.+++.++.++..
T Consensus       669 ~~l~~~l~~l~~~~~~l~~~i~~l~~~i~~  698 (880)
T PRK03918        669 LELSRELAGLRAELEELEKRREEIKKTLEK  698 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333444444444444443333

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

Probab=88.04  E-value=2.4  Score=32.61  Aligned_cols=33  Identities=30%  Similarity=0.423  Sum_probs=22.3

Q ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q 032660           33 LKQSTEDLQEKIKELKAEKNELRDEKQRLKADK   65 (136)
Q Consensus        33 Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~ek   65 (136)
                      ++.++..-..-|-.|+.|+|-|.||+-.|+.|.
T Consensus        87 fe~s~~qsLq~i~~L~nE~n~L~eEN~~L~eEl  119 (120)
T PF10482_consen   87 FESSHLQSLQHIFELTNEMNTLKEENKKLKEEL  119 (120)
T ss_pred             HHhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence            334443334446778888888888888887764

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

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

Probab=88.03  E-value=3.5  Score=27.88  Aligned_cols=51  Identities=18%  Similarity=0.283  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      |...+.+|....+-++..+.+|...--+...+..+|+.++..|..+++.+.
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            344455555555555555555555555555555555555555555565554

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.

>PF10226 DUF2216: Uncharacterized conserved proteins (DUF2216); InterPro: IPR019359 Proteins in this entry are found in Metazoa and contain a coiled-coil domain

Probab=87.99  E-value=2.7  Score=34.71  Aligned_cols=47  Identities=30%  Similarity=0.384  Sum_probs=34.5

Q ss_pred             chhhhHHHHHHHHH-------HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           11 DKATILSDVVRMME-------QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        11 DKAsIL~DAir~lk-------qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      +|-+++.+--++++       ....||..||+.|.+|+++.++|...++-|-|+
T Consensus        31 ek~~~m~~~g~lm~evNrrlQ~hl~EIR~LKe~NqkLqedNqELRdLCCFLDdd   84 (195)
T PF10226_consen   31 EKMSLMVEHGRLMKEVNRRLQQHLNEIRGLKEVNQKLQEDNQELRDLCCFLDDD   84 (195)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchh
Confidence            45555555555544       455788899999999999999998888877664

Some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed.

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

Probab=87.96  E-value=4.2  Score=36.35  Aligned_cols=48  Identities=23%  Similarity=0.376  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      ..+.|++++-++.++|.....+|+.=+++|+.++.+|+.+-..|+.++
T Consensus       222 r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~ni  269 (365)
T KOG2391|consen  222 RREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQKNI  269 (365)
T ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhhh
Confidence            445566666666666666666666666666666666666666655543

>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=87.95  E-value=1.9  Score=28.66  Aligned_cols=45  Identities=24%  Similarity=0.309  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      .|+.=..+||++-+.=.-+......+.++|+.||..|+++.++++
T Consensus         5 Rl~ELe~klkaerE~R~~d~~~a~~rl~~l~~EN~~Lr~eL~~~r   49 (52)
T PF12808_consen    5 RLEELERKLKAEREARSLDRSAARKRLSKLEGENRLLRAELERLR   49 (52)
T ss_pred             HHHHHHHHHHHhHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344445566666655555567777888888899999998888765

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 [, ].

>PF13747 DUF4164: Domain of unknown function (DUF4164)

Probab=87.94  E-value=3.5  Score=29.47  Aligned_cols=50  Identities=26%  Similarity=0.473  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .++++|..-+.+|......-.+..+.-    +++.+|-+.|..+..+|.++|-.
T Consensus         8 ~al~rL~~aid~LE~~v~~r~~~~~~~----~~~e~ei~~l~~dr~rLa~eLD~   57 (89)
T PF13747_consen    8 AALTRLEAAIDRLEKAVDRRLERDRKR----DELEEEIQRLDADRSRLAQELDQ   57 (89)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhh----hhHHHHHHHHHhhHHHHHHHHHh
Confidence            356777777777777665544443322    45555555555555555555443

>PF12777 MT: Microtubule-binding stalk of dynein motor; InterPro: IPR024743 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=87.80  E-value=5.6  Score=33.95  Aligned_cols=51  Identities=22%  Similarity=0.346  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEK   67 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~   67 (136)
                      ..+-.-|...+.+++++.+....|+.+......|+++|+++....+.-.++
T Consensus       231 ~~~~~~L~~~~~~l~~l~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~kl~r  281 (344)
T PF12777_consen  231 EEAEEQLAEKQAELAELEEKLAALQKEYEEAQKEKQELEEEIEETERKLER  281 (344)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            344445555555555555555555555555555555555544443333333

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules (D1-6), of which four correspond to the ATP binding sites with P-loop signatures, and two are modules in which the P loop has been lost in evolution. This domain occurs between D4 and D5 and includes the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [].; PDB: 3VKH_A 3VKG_A 3ERR_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 2RR7_A.

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

Probab=87.79  E-value=2.1  Score=32.60  Aligned_cols=42  Identities=31%  Similarity=0.444  Sum_probs=25.0

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      ..|+=+|......|......+|.|-=.||.|++.|-.=||+|
T Consensus        62 ItQVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNL  103 (120)
T KOG3650|consen   62 ITQVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENL  103 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHH
Confidence            334445555666666666666666666666666666666555

>smart00340 HALZ homeobox associated leucin zipper

Probab=87.78  E-value=2.2  Score=27.73  Aligned_cols=40  Identities=25%  Similarity=0.443  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccC-CCCCCCC
Q 032660           41 QEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA-PSGFLPH   84 (136)
Q Consensus        41 ~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~-~p~f~ph   84 (136)
                      +-+..+||.=.+.|-|||.+|+.|.    ++|+++.. ||-||++
T Consensus         4 EvdCe~LKrcce~LteeNrRL~ke~----~eLralk~~~~~~m~~   44 (44)
T smart00340        4 EVDCELLKRCCESLTEENRRLQKEV----QELRALKLSPPLYMQH   44 (44)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHhcccCCcccccC

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

Probab=87.78  E-value=4.7  Score=27.29  Aligned_cols=45  Identities=20%  Similarity=0.326  Sum_probs=32.2

Q ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccC
Q 032660           33 LKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA   77 (136)
Q Consensus        33 Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~   77 (136)
                      |.+.+..|+..+-++..-..+|-+.-.....+|++|+.+++.|..
T Consensus         2 le~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~   46 (69)
T PF04102_consen    2 LEERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRE   46 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456667777777777777777777777777777777777777654

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.

>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=87.74  E-value=6.7  Score=32.54  Aligned_cols=14  Identities=36%  Similarity=0.465  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHHHH
Q 032660           16 LSDVVRMMEQLRTE   29 (136)
Q Consensus        16 L~DAir~lkqLr~e   29 (136)
                      |.|...-...|..|
T Consensus        34 L~e~~kE~~~L~~E   47 (230)
T PF10146_consen   34 LEEYRKEMEELLQE   47 (230)
T ss_pred             HHHHHHHHHHHHHH
Confidence            44444444444433

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.

>PLN02320 seryl-tRNA synthetase

Probab=87.64  E-value=5.6  Score=36.66  Aligned_cols=53  Identities=25%  Similarity=0.382  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHH---------HHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIK---------ELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~---------~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .++|..|++.|+.+...+..+++         +|..|-.+|+++...|+.+...++.++..+
T Consensus       102 ~r~~~~~~~~lr~ern~~sk~i~~~~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~~~l~~~  163 (502)
T PLN02320        102 MLALQKEVERLRAERNAVANKMKGKLEPSERQALVEEGKNLKEGLVTLEEDLVKLTDELQLE  163 (502)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35566666666666666655553         455555666666666666666666666663

>PRK14160 heat shock protein GrpE; Provisional

Probab=87.56  E-value=2.9  Score=34.49  Aligned_cols=42  Identities=26%  Similarity=0.408  Sum_probs=27.6

Q ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           30 AQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        30 ~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      +..|++++..|.+++..|+.+..+|++...++.+|.++....
T Consensus        56 ~~~l~~e~~~l~~~l~~l~~e~~elkd~~lR~~AefeN~RKR   97 (211)
T PRK14160         56 IEELKDENNKLKEENKKLENELEALKDRLLRTVAEYDNYRKR   97 (211)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555556666666666666677777778888877766543

>PF12777 MT: Microtubule-binding stalk of dynein motor; InterPro: IPR024743 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=87.55  E-value=4.3  Score=34.61  Aligned_cols=54  Identities=24%  Similarity=0.383  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .-+...+.+++..+.+...+++++..|+.+.++...|+..|+.+++..+..|..
T Consensus       228 ~~l~~~~~~L~~~~~~l~~l~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~kl~r  281 (344)
T PF12777_consen  228 AELEEAEEQLAEKQAELAELEEKLAALQKEYEEAQKEKQELEEEIEETERKLER  281 (344)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            345666677777777777777777777777777777788888777777777765

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules (D1-6), of which four correspond to the ATP binding sites with P-loop signatures, and two are modules in which the P loop has been lost in evolution. This domain occurs between D4 and D5 and includes the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [].; PDB: 3VKH_A 3VKG_A 3ERR_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 2RR7_A.

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

Probab=87.44  E-value=4.1  Score=34.24  Aligned_cols=53  Identities=17%  Similarity=0.397  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      ...|+.++++...+++....++.+...|+.+...+..|.+.+...+.+++.++
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            34455555555555555555555555555555544444444444444444444

>PRK14127 cell division protein GpsB; Provisional

Probab=87.43  E-value=4.1  Score=30.54  Aligned_cols=32  Identities=34%  Similarity=0.478  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           44 IKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        44 ~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ...|..|..+|++|+.+|+.+++.++.++...
T Consensus        39 ye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~~   70 (109)
T PRK14127         39 YEAFQKEIEELQQENARLKAQVDELTKQVSVG   70 (109)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence            34445555566666666666666666666643

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

Probab=87.41  E-value=4.2  Score=31.14  Aligned_cols=36  Identities=25%  Similarity=0.496  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      -.+..++..|..++..+..+|.+|.....-|.++--
T Consensus        17 e~~e~~~K~le~~~~~~E~EI~sL~~K~~~lE~eld   52 (143)
T PF12718_consen   17 EELEAKVKQLEQENEQKEQEITSLQKKNQQLEEELD   52 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444433333333333

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].

>TIGR00606 rad50 rad50

Probab=87.40  E-value=3.6  Score=40.91  Aligned_cols=55  Identities=18%  Similarity=0.273  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      |+..+.-..+|..++.+|+.++..+.+++++++.+...|+.+...+.++.+++..
T Consensus       876 l~~~l~~r~~le~~L~el~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  930 (1311)
T TIGR00606       876 IGTNLQRRQQFEEQLVELSTEVQSLIREIKDAKEQDSPLETFLEKDQQEKEELIS  930 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHH
Confidence            3445666667777777777777777777766666666666666666665555443

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

>PRK05431 seryl-tRNA synthetase; Provisional

Probab=87.37  E-value=4  Score=36.09  Aligned_cols=57  Identities=25%  Similarity=0.422  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHH---HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQE---KIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~e---e~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ...-+.+||.|.+++-+++..+..   +..+|+.|-++|+++...|+.+...++.++..+
T Consensus        40 l~~~~~~lr~~rn~~sk~i~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~   99 (425)
T PRK05431         40 LQTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKELKEEIKALEAELDELEAELEEL   99 (425)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455678889998888888876432   356799999999999999999999999998884

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=87.33  E-value=3.5  Score=32.30  Aligned_cols=48  Identities=33%  Similarity=0.572  Sum_probs=32.4

Q ss_pred             HHHHHHHHHhhHHHHHH-------------HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           27 RTEAQKLKQSTEDLQEK-------------IKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee-------------~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |.||=+||..-.+|...             -++|..+|++|+.|.-.|+.|.+++..++.+
T Consensus        46 reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qqv~~L~~e~s~~~~E~da  106 (135)
T KOG4196|consen   46 REEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQVEKLKEENSRLRRELDA  106 (135)
T ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45777777777766554             3566777777777777777777766666655

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

Probab=87.32  E-value=3.6  Score=28.67  Aligned_cols=33  Identities=24%  Similarity=0.489  Sum_probs=15.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           37 TEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        37 n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      +..+..++..++.|.+.|++|+..|+.|+.+|.
T Consensus        37 ~~~~~~~l~~l~~~~~~l~~e~~~L~lE~~~l~   69 (97)
T PF04999_consen   37 SRQLFYELQQLEKEIDQLQEENERLRLEIATLS   69 (97)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            334444444444444444444444444444443

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

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=87.31  E-value=1.7  Score=36.61  Aligned_cols=40  Identities=28%  Similarity=0.442  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKAD   64 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~e   64 (136)
                      .|+.+++.|++.+..++.+.+.++.|.+++|++...++..
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   42 (364)
T TIGR01242         3 ELDVRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRSP   42 (364)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            4667888899999999999999998888888877655543

Many proteins may score above the trusted cutoff because an internal

>PRK04406 hypothetical protein; Provisional

Probab=87.24  E-value=8  Score=26.95  Aligned_cols=52  Identities=17%  Similarity=0.185  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      .|...+..|....+-++..|.+|...--+.+.+...|+.+...|-++++.+.
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            4566677777777777777777777666677777777777777777777654

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

Probab=87.23  E-value=4.4  Score=30.97  Aligned_cols=48  Identities=21%  Similarity=0.336  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +-.++..|.+....|..++..||+-.-+|-+||..|.-|-++|...|-
T Consensus         6 iFd~v~~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~   53 (114)
T COG4467           6 IFDQVDNLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLG   53 (114)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhC
Confidence            334555555666666666666666666666666666666666655443

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

Probab=87.21  E-value=5.6  Score=34.58  Aligned_cols=58  Identities=28%  Similarity=0.537  Sum_probs=23.8

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           12 KATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        12 KAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      |-.+|-+.+.-+++.|.   .|......+.++..+|..+..|+++.-..|+++...|..++
T Consensus        14 K~~~lk~~~~e~~ekR~---El~~~~~~~~ekRdeln~kvrE~~e~~~elr~~rdeineev   71 (294)
T COG1340          14 KRKQLKEEIEELKEKRD---ELRKEASELAEKRDELNAKVRELREKAQELREERDEINEEV   71 (294)
T ss_pred             HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33455555555555442   22333333333333333333344444444444444444333

>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=87.18  E-value=5.7  Score=30.90  Aligned_cols=28  Identities=25%  Similarity=0.399  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           47 LKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        47 L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ++.|..+|++|....+.|.+.|..|.+.
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

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

Probab=87.16  E-value=6.1  Score=31.81  Aligned_cols=47  Identities=28%  Similarity=0.445  Sum_probs=20.5

Q ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           28 TEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        28 ~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .++.+|+.....|++....++.+|.+.-.|..+|+++.+.|++++..
T Consensus       131 ~~i~~Le~ki~el~~~~~~~~~~ke~~~~ei~~lks~~~~l~~~~~~  177 (190)
T PF05266_consen  131 SEIKELEMKILELQRQAAKLKEKKEAKDKEISRLKSEAEALKEEIEN  177 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333444444433333334444444455555555555544443

>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=87.13  E-value=6.1  Score=31.46  Aligned_cols=27  Identities=48%  Similarity=0.642  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 032660           40 LQEKIKELKAEKNELRDEKQRLKADKE   66 (136)
Q Consensus        40 L~ee~~~L~~EKnELrdEk~~Lk~eke   66 (136)
                      +..++..|+.|+++|+.+...|+...+
T Consensus       125 l~~~i~~L~~e~~~L~~~~~~l~~~~e  151 (189)
T PF10211_consen  125 LEEEIEELEEEKEELEKQVQELKNKCE  151 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333333

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 [].

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=87.10  E-value=5.5  Score=36.59  Aligned_cols=20  Identities=10%  Similarity=0.302  Sum_probs=8.4

Q ss_pred             HHHHHhHHHHHHHHHHHHhc
Q 032660           56 DEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        56 dEk~~Lk~eke~Le~qlk~~   75 (136)
                      .++..++.+..+.+.+++.+
T Consensus       269 ~ei~~le~e~~e~~~~l~~l  288 (650)
T TIGR03185       269 RQLKEIEAARKANRAQLREL  288 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            33334444444444444443

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.

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

Probab=87.06  E-value=6.9  Score=26.43  Aligned_cols=48  Identities=21%  Similarity=0.404  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+++.+|......|..++..|..+-|-||.+-...|.|-.|-++.|--
T Consensus         2 ~akid~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN   49 (56)
T PF04728_consen    2 NAKIDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDN   49 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            357888999999999999999999999999999999888877766643

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.

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

Probab=86.97  E-value=4.3  Score=40.06  Aligned_cols=62  Identities=26%  Similarity=0.368  Sum_probs=45.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      |..+=--+++.|..+++.||..+..|+-++++|+.|-.++-.+++.|+.+-+.|+.||.-.+
T Consensus       658 ~~~kyK~lI~~lD~~~e~lkQ~~~~l~~e~eeL~~~vq~~~s~hsql~~q~~~Lk~qLg~~~  719 (970)
T KOG0946|consen  658 IQQKYKGLIRELDYQIENLKQMEKELQVENEELEEEVQDFISEHSQLKDQLDLLKNQLGIIS  719 (970)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            44444455666677777777777777777888887777777888888888888888887543

>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=86.96  E-value=7.3  Score=33.27  Aligned_cols=61  Identities=23%  Similarity=0.373  Sum_probs=42.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH-------HHHHHHHHHHHhc
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK-------ADKEKLEQQVKAM   75 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk-------~eke~Le~qlk~~   75 (136)
                      ++.+...-+.+++.++..|+.+..+|..+|+.-+.|..-.+.....|+       .|-|+||.+|+.+
T Consensus       170 ai~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~vRPAfmdEyEklE~EL~~l  237 (267)
T PF10234_consen  170 AIKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERNQKRLQSLQSVRPAFMDEYEKLEEELQKL  237 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHH
Confidence            344555566677777777777777777777777777666666666665       3778888888763

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 [].

>PRK15396 murein lipoprotein; Provisional

Probab=86.93  E-value=5.5  Score=28.27  Aligned_cols=43  Identities=23%  Similarity=0.482  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      |.+|.++++.|+.....|..++..       +|.+-..-+.|-+|-++.|
T Consensus        27 vd~LssqV~~L~~kvdql~~dv~~-------~~~~~~~a~~eA~raN~Rl   69 (78)
T PRK15396         27 IDQLSSDVQTLNAKVDQLSNDVNA-------MRSDVQAAKDDAARANQRL   69 (78)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHH
Confidence            345555555555555555554444       4444444444444444433

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

Probab=86.69  E-value=2.2  Score=35.55  Aligned_cols=35  Identities=31%  Similarity=0.439  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           40 LQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        40 L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |+++...++++.+-|++|-.....+.++++.+..+
T Consensus       149 ~~~~~~~~~~~~~kL~~el~~~~~~Le~~~~~~~a  183 (216)
T KOG1962|consen  149 LEEENDKLKADLEKLETELEKKQKKLEKAQKKVDA  183 (216)
T ss_pred             hhhhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45555555555555555555555555555444444

>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)

Probab=86.69  E-value=1.7  Score=30.57  Aligned_cols=31  Identities=32%  Similarity=0.470  Sum_probs=15.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 032660           36 STEDLQEKIKELKAEKNELRDEKQRLKADKE   66 (136)
Q Consensus        36 ~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke   66 (136)
                      +...|+++++.|+.++..+++++..+++++.
T Consensus        71 ~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~  101 (104)
T PF13600_consen   71 ELKELEEELEALEDELAALQDEIQALEAQIA  101 (104)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444555555555555544444

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

Probab=86.63  E-value=3.2  Score=30.46  Aligned_cols=39  Identities=26%  Similarity=0.530  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKAD   64 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~e   64 (136)
                      |..+++.|++.+..++++++.|+.+..++.+|...||.|
T Consensus        78 L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E  116 (118)
T PF13815_consen   78 LSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKE  116 (118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            455555666666666666666666666665655555554

>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=86.52  E-value=8.4  Score=26.50  Aligned_cols=49  Identities=18%  Similarity=0.455  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEK   67 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~   67 (136)
                      .+..++.|+.-++++.+....++++...+..|-+++-.+-..+..+...
T Consensus        17 l~~~l~~l~~~l~~~~~ti~~l~~~~~~i~~e~~~ll~~~n~l~~dv~~   65 (90)
T PF06103_consen   17 LIKVLKKLKKTLDEVNKTIDTLQEQVDPITKEINDLLHNTNELLEDVNE   65 (90)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455566666666666666666666666666655555555555544433

>PRK02119 hypothetical protein; Provisional

Probab=86.46  E-value=4.4  Score=28.04  Aligned_cols=47  Identities=21%  Similarity=0.188  Sum_probs=30.1

Q ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           29 EAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        29 e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ++..+.+....|+..+-....-..+|-+.-.....+|++|+.|++.|
T Consensus         3 ~~~~~e~Ri~~LE~rla~QE~tie~LN~~v~~Qq~~id~L~~ql~~L   49 (73)
T PRK02119          3 IQQNLENRIAELEMKIAFQENLLEELNQALIEQQFVIDKMQVQLRYM   49 (73)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44556666666666666666666666666666666666666666665

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

Probab=86.42  E-value=2.9  Score=38.99  Aligned_cols=38  Identities=26%  Similarity=0.483  Sum_probs=16.1

Q ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           32 KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      .|++++..+...++.|..|+..|+.|+.+|..++.++-
T Consensus       152 ~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r  189 (546)
T KOG0977|consen  152 ELEAEINTLKRRIKALEDELKRLKAENSRLREELARAR  189 (546)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence            33344444444444444444444444444444444333

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

Probab=86.29  E-value=5.5  Score=30.49  Aligned_cols=59  Identities=19%  Similarity=0.389  Sum_probs=46.0

Q ss_pred             HHHHHHH-HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           17 SDVVRMM-EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        17 ~DAir~l-kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +++++-- +.|..+++.|-...+...|-++..+.|-+|+|++-..++.|++.+++-+..|
T Consensus        56 s~~l~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv~~i~~dv~~v~~~V~~L  115 (126)
T PF07889_consen   56 SESLSSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDVSQIGDDVDSVQQMVEGL  115 (126)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence            4444433 3577788888888888888888888899999999999999888888776664

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

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

Probab=86.25  E-value=6.5  Score=35.69  Aligned_cols=18  Identities=17%  Similarity=0.403  Sum_probs=8.0

Q ss_pred             HHHhHHHHHHHHHHHHhc
Q 032660           58 KQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        58 k~~Lk~eke~Le~qlk~~   75 (136)
                      ...++.+|+.++..++.+
T Consensus        89 l~~~~~~I~~~~~~l~~l  106 (420)
T COG4942          89 LKKLRKQIADLNARLNAL  106 (420)
T ss_pred             HHHHHhhHHHHHHHHHHH
Confidence            334444444444444444

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

Probab=86.24  E-value=4  Score=38.47  Aligned_cols=52  Identities=29%  Similarity=0.514  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHH-----------------HHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELK-----------------AEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~-----------------~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      .|.+|.+|+++-.++++.|+.++.+|+                 .|+|+|..+...++.++++|.+.+.
T Consensus       295 ~l~~l~~Eie~kEeE~e~lq~~~d~Lk~~Ie~Q~iS~~dve~mn~Er~~l~r~l~~i~~~~d~l~k~vw  363 (581)
T KOG0995|consen  295 KLEMLKSEIEEKEEEIEKLQKENDELKKQIELQGISGEDVERMNLERNKLKRELNKIQSELDRLSKEVW  363 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355566666666666666666554443                 4666776666666666666665443

>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea

Probab=86.20  E-value=3.5  Score=29.42  Aligned_cols=45  Identities=18%  Similarity=0.382  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      .+.-.=...|++..+.+..+++.++.+..++.++-..|+.++.++
T Consensus        59 ~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk~~l~~~  103 (105)
T cd00632          59 QEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQEKIQQA  103 (105)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444555666666666666666666666666666666665554

Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st

>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=86.18  E-value=1.1  Score=30.78  Aligned_cols=29  Identities=34%  Similarity=0.550  Sum_probs=13.9

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELR   55 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELr   55 (136)
                      |.|++-||+.+..|++.+..|+.|-+=||
T Consensus        13 rEEVevLK~~I~eL~~~n~~Le~EN~~Lk   41 (59)
T PF01166_consen   13 REEVEVLKEQIAELEERNSQLEEENNLLK   41 (59)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444

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.

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

Probab=86.05  E-value=9.1  Score=30.11  Aligned_cols=51  Identities=24%  Similarity=0.468  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      +|+.-..++..++..|+.....+...+..|+....+|+.....++++++.|
T Consensus        88 ~al~~k~~~e~~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl~e~k~k~~~l  138 (221)
T PF04012_consen   88 EALQRKADLEEQAERLEQQLDQAEAQVEKLKEQLEELEAKLEELKSKREEL  138 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444445555555555555555444444444444444444444444433333

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 [].

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

Probab=86.04  E-value=2.2  Score=35.66  Aligned_cols=59  Identities=22%  Similarity=0.344  Sum_probs=47.6

Q ss_pred             chhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           11 DKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        11 DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      +=.+||.=-+.==...|....+|++++..++.++..|+.|.+.||.+|..|=..+-=|+
T Consensus        76 ~~~siLpIVtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylq  134 (248)
T PF08172_consen   76 GDSSILPIVTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQ  134 (248)
T ss_pred             CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45667765555556789999999999999999999999999999999999975554444

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

>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus

Probab=85.81  E-value=1.5  Score=39.31  Aligned_cols=26  Identities=31%  Similarity=0.454  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELK   48 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~   48 (136)
                      .-.||.|-.+||+||+.|..|...|+
T Consensus        34 ~~aLr~EN~~LKkEN~~Lk~eVerLE   59 (420)
T PF07407_consen   34 NFALRMENHSLKKENNDLKIEVERLE   59 (420)
T ss_pred             hhhHHHHhHHHHHHHHHHHHHHHHHH
Confidence            34566666666666666666655553

Members of this family are typically of around 420 residues in length. The function of this family is unknown.

>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=85.80  E-value=9.3  Score=26.29  Aligned_cols=56  Identities=13%  Similarity=0.303  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      |-..-+.+++++.-+++++++...+..++..+-.+-|++-++-..-....+.+-+.
T Consensus        21 l~~l~~~l~~~~~ti~~l~~~~~~i~~e~~~ll~~~n~l~~dv~~k~~~v~~~~~~   76 (90)
T PF06103_consen   21 LKKLKKTLDEVNKTIDTLQEQVDPITKEINDLLHNTNELLEDVNEKLEKVDPVFEA   76 (90)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence            44555667777777777777777777777777777777776655544444444333

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

Probab=85.78  E-value=10  Score=27.63  Aligned_cols=45  Identities=16%  Similarity=0.378  Sum_probs=24.8

Q ss_pred             HHHHHhhHHHHHHHHHH--HHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           31 QKLKQSTEDLQEKIKEL--KAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        31 ~~Lk~~n~~L~ee~~~L--~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .+.......++.+++.|  ..+-+.|+-+-+.++-++..++.+++.+
T Consensus        45 ~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v   91 (106)
T PF10805_consen   45 DEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGV   91 (106)
T ss_pred             HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            33355555555555555  5555555555555555555555555554

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

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

Probab=85.69  E-value=1.3  Score=34.36  Aligned_cols=22  Identities=27%  Similarity=0.354  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDL   40 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L   40 (136)
                      ..+-.++||.|+++|++|+.++
T Consensus        38 ~~~~~~~l~~Ei~~l~~E~~~i   59 (161)
T PF04420_consen   38 SSKEQRQLRKEILQLKRELNAI   59 (161)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTS
T ss_pred             ccHHHHHHHHHHHHHHHHHHcC
Confidence            3344556666666666655443

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

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=85.62  E-value=5.6  Score=36.78  Aligned_cols=34  Identities=29%  Similarity=0.457  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      ++++.+-.......|+.+++.+..|++++||++.
T Consensus       373 ~e~~kk~~e~k~~q~q~k~~k~~kel~~~~E~n~  406 (493)
T KOG0804|consen  373 LEAEKKIVERKLQQLQTKLKKCQKELKEEREENK  406 (493)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333444444445555555555555444

>PRK00846 hypothetical protein; Provisional

Probab=85.50  E-value=11  Score=26.78  Aligned_cols=52  Identities=13%  Similarity=0.100  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      ++...+..|....+-.+.-|.+|...--+.+.+..+|+.++..|-.+|+.+.
T Consensus        10 ~le~Ri~~LE~rlAfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~~   61 (77)
T PRK00846         10 ALEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKVR   61 (77)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3455666666666666666777777777777777777777777777787764

>PF08647 BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR013956 BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions []

Probab=85.50  E-value=4.9  Score=28.73  Aligned_cols=55  Identities=22%  Similarity=0.283  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .--++++..+.++..+...+++.+-.|..||+-=..+--.+...++.|..+++.+
T Consensus        10 ~a~~~~~~~~~~k~~~~~~lE~k~~rl~~Ek~kadqkyfa~mr~~d~l~~e~k~L   64 (96)
T PF08647_consen   10 QAFKELSEQADKKVKELTILEQKKLRLEAEKAKADQKYFAAMRSKDALDNEMKKL   64 (96)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            3345666666666666666666666666666655555555555555555555554

>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]

Probab=85.50  E-value=3.4  Score=34.85  Aligned_cols=12  Identities=42%  Similarity=0.675  Sum_probs=5.3

Q ss_pred             HHHHHHHHHHhH
Q 032660           51 KNELRDEKQRLK   62 (136)
Q Consensus        51 KnELrdEk~~Lk   62 (136)
                      .+.|++||.+|+
T Consensus        92 ~~~l~~EN~~Lr  103 (284)
T COG1792          92 VESLEEENKRLK  103 (284)
T ss_pred             HHHHHHHHHHHH
Confidence            334444444444

>PRK00295 hypothetical protein; Provisional

Probab=85.45  E-value=9.3  Score=26.00  Aligned_cols=50  Identities=16%  Similarity=0.168  Sum_probs=33.5

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      ...+.+|....+-.+..|.+|...--+...+...|+.+...|.++++.+.
T Consensus         4 e~Ri~~LE~kla~qE~tie~Ln~~v~~Qq~~I~~L~~ql~~L~~rl~~~~   53 (68)
T PRK00295          4 EERVTELESRQAFQDDTIQALNDVLVEQQRVIERLQLQMAALIKRQEEMV   53 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            34466666666666666666666666666666777777777777777764

>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function

Probab=85.41  E-value=6.8  Score=28.42  Aligned_cols=31  Identities=29%  Similarity=0.376  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEK   51 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EK   51 (136)
                      -++--+.=++.+++.+|++|++++..|+.||
T Consensus        16 ~i~~y~~~k~~ka~~~~~kL~~en~qlk~Ek   46 (87)
T PF10883_consen   16 LILAYLWWKVKKAKKQNAKLQKENEQLKTEK   46 (87)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444455556666666666665555555443

>KOG0982 consensus Centrosomal protein Nuf [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=85.41  E-value=5.3  Score=36.91  Aligned_cols=38  Identities=34%  Similarity=0.450  Sum_probs=22.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           36 STEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        36 ~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +++.|+-.++-|..|-.|||...++||+.+++|....+
T Consensus       298 e~Enlqmr~qqleeentelRs~~arlksl~dklaee~q  335 (502)
T KOG0982|consen  298 EKENLQMRDQQLEEENTELRSLIARLKSLADKLAEEDQ  335 (502)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            45555555666666666666666666666666655443

>PRK02224 chromosome segregation protein; Provisional

Probab=85.38  E-value=6.8  Score=36.59  Aligned_cols=47  Identities=34%  Similarity=0.504  Sum_probs=20.6

Q ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           28 TEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        28 ~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+++.+..+...+++++..+..+.++++++...++..+++++.++..
T Consensus       251 ~~l~~l~~~~~~l~~~i~~~e~~~~~l~~~i~~~~~~~~~le~e~~~  297 (880)
T PRK02224        251 EELETLEAEIEDLRETIAETEREREELAEEVRDLRERLEELEEERDD  297 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444444444444443333

>PF01763 Herpes_UL6: Herpesvirus UL6 like; InterPro: IPR002660 This family consists of various proteins from the Herpesviridae that are similar to Human herpesvirus 1 (HHV-1) UL6 virion protein

Probab=85.17  E-value=3.4  Score=38.62  Aligned_cols=35  Identities=29%  Similarity=0.533  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      |+++-.+|+.||++|..++.++++++.|....++|
T Consensus       372 In~qf~tIe~Lk~~n~~~~~kl~~~e~~L~r~~~~  406 (557)
T PF01763_consen  372 INNQFDTIEDLKEENQDLEKKLRELESELSRYREE  406 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44444444444444444444444444444444443

UL6 is essential for cleavage and packaging of the viral genome [].; GO: 0006323 DNA packaging

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

Probab=85.16  E-value=7.6  Score=28.68  Aligned_cols=40  Identities=23%  Similarity=0.265  Sum_probs=25.1

Q ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           32 KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      .+...+..++..+..+.+|-..|..++..|++++.+|++.
T Consensus        47 ~~~~~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg   86 (117)
T COG2919          47 NGAADVLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG   86 (117)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            3444555566666666666666666666666666666665

>KOG4571 consensus Activating transcription factor 4 [Transcription]

Probab=85.14  E-value=3.2  Score=36.10  Aligned_cols=50  Identities=22%  Similarity=0.349  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .|+||=+       |-|++-+.|..+++.|+.+-.+||+.-.+|+.||..|.+-+..
T Consensus       238 AAtRYRq-------KkRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e  287 (294)
T KOG4571|consen  238 AATRYRQ-------KKRAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILE  287 (294)
T ss_pred             HHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6777744       4455666666777777777777777777777777777766554

>PRK02793 phi X174 lysis protein; Provisional

Probab=85.10  E-value=10  Score=26.10  Aligned_cols=51  Identities=20%  Similarity=0.204  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      +...+.+|....+-.+..|.+|...--+.+.+...|+.+...|-++++.+.
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            556677777777777777777777777777777777777777777777764

>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=85.09  E-value=2.8  Score=33.01  Aligned_cols=29  Identities=21%  Similarity=0.522  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           46 ELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        46 ~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+..|+.+|+.....|+++...|+..++.
T Consensus        86 ~~~~e~k~L~~~v~~Le~e~r~L~~~~~~  114 (158)
T PF09744_consen   86 QWRQERKDLQSQVEQLEEENRQLELKLKN  114 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            44455555555555555555555544444

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

>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=85.00  E-value=3.8  Score=34.78  Aligned_cols=31  Identities=19%  Similarity=0.430  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELR   55 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELr   55 (136)
                      +|+.++.++.+...+|+.|++.+...-|..+
T Consensus        54 ~L~~e~~s~Q~~~~~L~~ev~~~~~~~~s~~   84 (247)
T COG3879          54 DLVKELRSLQKKVNTLAAEVEDLENKLDSVR   84 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444444444444444

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

Probab=84.91  E-value=4  Score=40.87  Aligned_cols=54  Identities=24%  Similarity=0.445  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      -|..|+.++.+|+++...+.++++....|+...+.+...|+..|+....+|+.+
T Consensus       409 evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~l~k~i~~~~~~l~~l  462 (1074)
T KOG0250|consen  409 EVEKLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQLRKKIENISEELKDL  462 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356678888999999999999999999999889889999999998888888775

>PRK14148 heat shock protein GrpE; Provisional

Probab=84.89  E-value=4.2  Score=33.06  Aligned_cols=40  Identities=28%  Similarity=0.488  Sum_probs=32.5

Q ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           34 KQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        34 k~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      ..+++.|++++..|+.|..+|++...++.+|.+++....+
T Consensus        39 ~~e~~~l~~~l~~l~~e~~elkd~~lR~~Ae~eN~rKR~~   78 (195)
T PRK14148         39 EEQLERAKDTIKELEDSCDQFKDEALRAKAEMENIRKRAE   78 (195)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4457888888899999999999999999999888765433

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

Probab=84.83  E-value=7.1  Score=34.21  Aligned_cols=59  Identities=20%  Similarity=0.316  Sum_probs=48.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhhHH-----HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           13 ATILSDVVRMMEQLRTEAQKLKQSTED-----LQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        13 AsIL~DAir~lkqLr~e~~~Lk~~n~~-----L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      +-|.++.+...-+||.+.+++-+.+-.     -++++.++-...-|||.|..+|+.+++.|+.+
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            568899999999999999887765443     36888999999999999999999998888754

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.

>PRK03947 prefoldin subunit alpha; Reviewed

Probab=84.68  E-value=5.3  Score=29.53  Aligned_cols=42  Identities=36%  Similarity=0.533  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      +.|.+|..+.+.|+.+.+.|+.++..|....+|++.=+..|+
T Consensus         6 ~~l~~l~~~~~~l~~~~~~l~~~~~~l~~~~~e~~~~~e~l~   47 (140)
T PRK03947          6 QELEELAAQLQALQAQIEALQQQLEELQASINELDTAKETLE   47 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456777777777777777777777777777666655444443

>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length

Probab=84.55  E-value=1.6  Score=29.65  Aligned_cols=23  Identities=26%  Similarity=0.406  Sum_probs=17.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHh
Q 032660           52 NELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        52 nELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .||.+....|++||+|++.++..
T Consensus        24 ~EL~~RIa~L~aEI~R~~~~~~~   46 (59)
T PF06698_consen   24 EELEERIALLEAEIARLEAAIAK   46 (59)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            57777778888888888877765

The function of this family is unknown.

>PRK04325 hypothetical protein; Provisional

Probab=84.50  E-value=6.4  Score=27.21  Aligned_cols=45  Identities=13%  Similarity=0.214  Sum_probs=22.9

Q ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           31 QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        31 ~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +.+.+.+..|+..+-....-..+|-+.-.....+|++|+.|++.|
T Consensus         5 ~~~e~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L   49 (74)
T PRK04325          5 QEMEDRITELEIQLAFQEDLIDGLNATVARQQQTLDLLQAQLRLL   49 (74)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444555555555555555555555555555555555555544

>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein

Probab=84.47  E-value=13  Score=28.25  Aligned_cols=16  Identities=25%  Similarity=0.551  Sum_probs=6.0

Q ss_pred             HHHHHHHHHHhhHHHH
Q 032660           26 LRTEAQKLKQSTEDLQ   41 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~   41 (136)
                      |.....+|+.++..|.
T Consensus        32 l~~~~~~l~~e~~~l~   47 (136)
T PF04871_consen   32 LEQENKRLEAEEKELK   47 (136)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3333333333333333

This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane

>PF09766 FimP: Fms-interacting protein; InterPro: IPR019163 This entry represents Thoc5 which is one of the subunits of the THO complex, which additionally contains: HPR1, Thoc2, Thoc6 and Thoc7

Probab=84.44  E-value=5.8  Score=34.39  Aligned_cols=52  Identities=29%  Similarity=0.457  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      -.||.+|.-|.+.    -..|.++.++|+.+|..|..|+...+.....|..+|+.+
T Consensus        90 ~lml~RL~~EL~~----Rk~L~~~~~el~~~k~~l~~~~~~k~~~L~~l~~~L~~l  141 (355)
T PF09766_consen   90 QLMLARLEFELEQ----RKRLEEQLKELEQRKKKLQQENKKKKKFLDSLPPQLKSL  141 (355)
T ss_pred             HHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence            4577778777654    446778888888888888888888888888888888875

The evolutionarily conserved multisubunit THO complex, which is recruited to actively transcribed genes is required for the efficient expression of genes that have internal tandem repeats. It is suggested that the THO complex functions to rectify aberrant structures that arise during transcription [, ] and is required for cell proliferation and for proper export of heat-shock mRNAs under heat stress []. This entry also identifies the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes [].

>PRK02224 chromosome segregation protein; Provisional

Probab=84.34  E-value=7.7  Score=36.23  Aligned_cols=21  Identities=24%  Similarity=0.330  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhh
Q 032660           17 SDVVRMMEQLRTEAQKLKQST   37 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n   37 (136)
                      .++.+=+..|+.++++|++..
T Consensus       533 e~~~~~~~~l~~e~~~l~~~~  553 (880)
T PRK02224        533 EEKRERAEELRERAAELEAEA  553 (880)
T ss_pred             HhHHHHHHHHHHHHHHHHHHH
Confidence            334444444455555544444

>PF14193 DUF4315: Domain of unknown function (DUF4315)

Probab=84.33  E-value=3.7  Score=29.43  Aligned_cols=48  Identities=33%  Similarity=0.549  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCCC
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS   79 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~~p   79 (136)
                      +..++.++++-++.+..+|...+.|...|-|+..         ..+-+-+++|+..|
T Consensus         3 leKi~~eieK~k~Kiae~Q~rlK~Le~qk~E~EN---------~EIv~~VR~~~mtp   50 (83)
T PF14193_consen    3 LEKIRAEIEKTKEKIAELQARLKELEAQKTEAEN---------LEIVQMVRSMKMTP   50 (83)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHcCCCH
Confidence            4678889999999999999999988887776532         22334566665544

>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []

Probab=84.31  E-value=8.5  Score=33.59  Aligned_cols=55  Identities=25%  Similarity=0.404  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHH---HHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIK---ELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~---~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      -.+++.|..++++|.++.+.|.++..   ..+..+++|.++..++..+|++++.-++.
T Consensus       241 ~~~~~~l~~~~~~~~~~i~~l~~~l~~~~k~~~k~~~~~~q~~~~~k~~~~~~~~~~~  298 (406)
T PF02388_consen  241 KEYLESLQEKLEKLEKEIEKLEEKLEKNPKKKNKLKELEEQLASLEKRIEEAEELIAE  298 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH-THHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            35788888888888888888887643   34456677778888888888888776554

These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.

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

Probab=84.25  E-value=4.6  Score=38.38  Aligned_cols=36  Identities=36%  Similarity=0.515  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      =.+||-.|+.+|+.+....+|.++.|+.|..|||..
T Consensus       546 r~~~lE~E~~~lr~elk~kee~~~~~e~~~~~lr~~  581 (697)
T PF09726_consen  546 RRRQLESELKKLRRELKQKEEQIRELESELQELRKY  581 (697)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346777888888888888888888888888777764

; GO: 0016021 integral to membrane

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

Probab=84.24  E-value=18  Score=28.39  Aligned_cols=47  Identities=26%  Similarity=0.444  Sum_probs=30.8

Q ss_pred             HHHHHHHH---HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           16 LSDVVRMM---EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        16 L~DAir~l---kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      |..++..|   .++..+|+.|++++..|.+.++.+-.+..+.|.+...+-
T Consensus        14 L~~~L~~l~~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~   63 (188)
T PF10018_consen   14 LSSALEELQEHQENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLP   63 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444   456677777777777777777777777777776665543

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

>COG5493 Uncharacterized conserved protein containing a coiled-coil domain [Function unknown]

Probab=84.16  E-value=6.6  Score=33.08  Aligned_cols=63  Identities=27%  Similarity=0.438  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH-------HHHHHhHHHHHHHHHHHHhccCCCCCCC
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR-------DEKQRLKADKEKLEQQVKAMSAPSGFLP   83 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELr-------dEk~~Lk~eke~Le~qlk~~~~~p~f~p   83 (136)
                      +-|.+|+.+.+..+.+.+.+-.|.+.-+++|.+|.       ++.-+++.++.+||.-+.++.+.=|.+.
T Consensus        46 ~dve~l~~e~E~~~k~l~de~~E~r~~~~tke~lk~l~~~~~~~f~a~~edi~rlE~~i~~lgaRwGils  115 (231)
T COG5493          46 QDVEELRKETEQRQKELADEKLEVRKQKATKEDLKLLQRFQEEEFRATKEDIKRLETIITGLGARWGILS  115 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            57788899999999988887777777777777776       6777899999999988888766544443

>PF14257 DUF4349: Domain of unknown function (DUF4349)

Probab=84.11  E-value=6.8  Score=31.79  Aligned_cols=50  Identities=26%  Similarity=0.373  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHH--HHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKE--LKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~--L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |+.++++.|+++.+.|++=.+.  =..+.-+++.|..+.+.|||.++.|++.
T Consensus       136 D~~arl~~l~~~~~rl~~ll~ka~~~~d~l~ie~~L~~v~~eIe~~~~~~~~  187 (262)
T PF14257_consen  136 DLEARLKNLEAEEERLLELLEKAKTVEDLLEIERELSRVRSEIEQLEGQLKY  187 (262)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444454444444444432211  0122334444555555555555555554

>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)

Probab=84.10  E-value=1.7  Score=30.61  Aligned_cols=37  Identities=32%  Similarity=0.412  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           38 EDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ....++++.|+.+..+|++++..+..++.-++.+++.
T Consensus        66 ~~~~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~  102 (104)
T PF13600_consen   66 ESDSPELKELEEELEALEDELAALQDEIQALEAQIAF  102 (104)
T ss_pred             ccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3445566666666666666666666666666666554

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=84.00  E-value=12  Score=28.79  Aligned_cols=51  Identities=29%  Similarity=0.482  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +..+..+...++.++...++.+..+..+.+.+..+...++.+..+|..+.-
T Consensus        86 l~~~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~~~~~~~l~~~~~  136 (177)
T PF13870_consen   86 LHFLSEELERLKQELKDREEELAKLREELYRVKKERDKLRKQNKKLRQQGG  136 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            333444444444444444444444444444444444444444444444433

>KOG4348 consensus Adaptor protein CMS/SETA [Signal transduction mechanisms]

Probab=83.97  E-value=4.8  Score=37.61  Aligned_cols=51  Identities=31%  Similarity=0.474  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHH-HHHHHHHHHHHHHHH---HhHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKI-KELKAEKNELRDEKQ---RLKADKEKLEQQV   72 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~-~~L~~EKnELrdEk~---~Lk~eke~Le~ql   72 (136)
                      -|..||+|+-+|..-.+.|...- ++|+.=+.+|.+||.   .|+-|+++|..-+
T Consensus       570 s~delr~qi~el~~ive~lk~~~~kel~kl~~dleeek~mr~~lemei~~lkka~  624 (627)
T KOG4348|consen  570 SLDELRAQIIELLCIVEALKKDHGKELEKLRKDLEEEKTMRSNLEMEIEKLKKAV  624 (627)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHhhHHHHHHHh
Confidence            47899999999999999998764 788888999999986   6888888887544

>PF15188 CCDC-167: Coiled-coil domain-containing protein 167

Probab=83.91  E-value=6.3  Score=28.50  Aligned_cols=48  Identities=19%  Similarity=0.354  Sum_probs=35.4

Q ss_pred             HHHHHHHHhhHHHHHHHHHHH---------H-HHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           28 TEAQKLKQSTEDLQEKIKELK---------A-EKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        28 ~e~~~Lk~~n~~L~ee~~~L~---------~-EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .||+.|.+........+..+.         . .+.+|.+|+..|+...++.|.||+.+
T Consensus         5 ~eId~lEekl~~cr~~le~ve~rL~~~eLs~e~R~~lE~E~~~l~~~l~~~E~eL~~L   62 (85)
T PF15188_consen    5 KEIDGLEEKLAQCRRRLEAVESRLRRRELSPEARRSLEKELNELKEKLENNEKELKLL   62 (85)
T ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHcccCCChHHHHHHHHHHHHHHHHhhccHHHHHHH
Confidence            466666666666665554433         2 56788899999999999999999986

>PF05700 BCAS2: Breast carcinoma amplified sequence 2 (BCAS2); InterPro: IPR008409 This family consists of several eukaryotic sequences of unknown function

Probab=83.87  E-value=10  Score=30.67  Aligned_cols=32  Identities=22%  Similarity=0.388  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           44 IKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        44 ~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +++|..+-.++-..+..++....+|++|++.+
T Consensus       177 L~~Le~~W~~~v~kn~eie~a~~~Le~ei~~l  208 (221)
T PF05700_consen  177 LRYLEQRWKELVSKNLEIEVACEELEQEIEQL  208 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455444555555555556666666665543

The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins []. BCAS2 is a putative spliceosome associated protein [].

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

Probab=83.77  E-value=7  Score=35.19  Aligned_cols=44  Identities=23%  Similarity=0.337  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEK   67 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~   67 (136)
                      .+|..=+.+++++|..|+-...+++.|++|-.+|.+.|-.|..+
T Consensus       130 q~LE~li~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE  173 (401)
T PF06785_consen  130 QHLEGLIRHLREENQCLQLQLDALQQECGEKEEESQTLNRELAE  173 (401)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHH
Confidence            44555566777788888888888888888888888888655443

>TIGR00414 serS seryl-tRNA synthetase

Probab=83.72  E-value=8.4  Score=34.05  Aligned_cols=57  Identities=25%  Similarity=0.422  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHH---HH-HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQ---EK-IKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~---ee-~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .+.-+.+||.|-+++-+++..+.   ++ ..+|+.+-.+|+++...|+.+...++.++..+
T Consensus        42 ~~~~~~~l~~erN~~sk~i~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~  102 (418)
T TIGR00414        42 LLSEIEELQAKRNELSKQIGKAKGQKKDKIEEIKKELKELKEELTELSAALKALEAELQDK  102 (418)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45557788888888888776643   22 67889999999999999999999999988884

This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.

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

Probab=83.68  E-value=16  Score=28.80  Aligned_cols=56  Identities=29%  Similarity=0.462  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +.-.-+..|..+++.+......|...++.|+....+++.++..|++....-+.+.+
T Consensus        95 ~~e~~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl~e~k~k~~~l~ar~~~a~a~~~  150 (221)
T PF04012_consen   95 DLEEQAERLEQQLDQAEAQVEKLKEQLEELEAKLEELKSKREELKARENAAKAQKK  150 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444556666666666666666666666666666666666666666665555544

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 [].

>TIGR02977 phageshock_pspA phage shock protein A

Probab=83.63  E-value=13  Score=29.75  Aligned_cols=54  Identities=22%  Similarity=0.351  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ..+..|..++..++.....|+..++.|+.+..+++..+..|.+.....+.+.+.
T Consensus        99 ~~~~~l~~~~~~~~~~v~~l~~~l~~L~~ki~~~k~k~~~l~ar~~~A~a~~~~  152 (219)
T TIGR02977        99 ELAEALERELAAVEETLAKLQEDIAKLQAKLAEARARQKALAIRHQAASSRLDV  152 (219)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445556666666666666666666666666666666666666665555554443

Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.

>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.61  E-value=5.7  Score=33.75  Aligned_cols=50  Identities=24%  Similarity=0.398  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH----HHHHHHHHHHHh
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK----ADKEKLEQQVKA   74 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk----~eke~Le~qlk~   74 (136)
                      .+|++..+|.+++.++|++...|..|.+.|...-.+.+    +..--||.++..
T Consensus        47 ~~~~r~~~L~~e~~s~Q~~~~~L~~ev~~~~~~~~s~~~~~~t~~~~ie~~l~~  100 (247)
T COG3879          47 VRRARDLDLVKELRSLQKKVNTLAAEVEDLENKLDSVRRSVLTDDAALEDRLEK  100 (247)
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHH
Confidence            45666778888888888888888888888887777777    444455555555

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=83.57  E-value=5.7  Score=36.74  Aligned_cols=52  Identities=12%  Similarity=0.221  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHhhHHHHHH----HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           24 EQLRTEAQKLKQSTEDLQEK----IKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee----~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +++.+|.+.++++|..|.+.    +..|+....-+.+.+.....+|..||.||+-+
T Consensus       392 ~k~~kel~~~~E~n~~l~knq~vw~~kl~~~~e~~~~~~~s~d~~I~dLqEQlrDl  447 (493)
T KOG0804|consen  392 KKCQKELKEEREENKKLIKNQDVWRGKLKELEEREKEALGSKDEKITDLQEQLRDL  447 (493)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            34444444455555555444    23444444455566667777888899998874

>PF04136 Sec34: Sec34-like family ; InterPro: IPR007265 Sec34 and Sec35 form a sub-complex in a seven-protein complex that includes Dor1

Probab=83.29  E-value=16  Score=28.34  Aligned_cols=56  Identities=16%  Similarity=0.340  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +.-+......++.|.+......++...|...+++|-+|+.+|..=.+.|...|+-+
T Consensus        20 l~~~~~~~~~l~~l~~~~~~Vs~kT~~l~~~ce~Ll~eq~~L~~~ae~I~~~L~yF   75 (157)
T PF04136_consen   20 LDQTDEILDQLDELQEQYNSVSEKTNSLHEACEQLLEEQTRLEELAEEISEKLQYF   75 (157)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence            44456667778888889999999999999999999999999999988888877763

This complex is thought to be important for tethering vesicles to the Golgi [].; GO: 0006886 intracellular protein transport, 0005801 cis-Golgi network, 0016020 membrane

>PF06657 Cep57_MT_bd: Centrosome microtubule-binding domain of Cep57; InterPro: IPR010597 This entry is thought to represent a centrosomal protein of 57 kDa (Cep57-related protein)

Probab=83.24  E-value=13  Score=26.11  Aligned_cols=56  Identities=20%  Similarity=0.365  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHH-----HHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELK-----AEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~-----~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      =..+|+.|+.|...|+-++..|+++.+.+.     ..+++|..+...|-..+|.=..|+-.
T Consensus        15 Ls~vl~~LqDE~~hm~~e~~~L~~~~~~~d~s~~~~~R~~L~~~l~~lv~~mE~K~dQI~~   75 (79)
T PF06657_consen   15 LSEVLKALQDEFGHMKMEHQELQDEYKQMDPSLGRRKRRDLEQELEELVKRMEAKADQIYK   75 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            367899999999999999999998887765     35555555555555555555555543

It is required for spindle microtubule attachment to both kinetochores and centrosomes and functions to tether minus-ends of spindle microtubules to centrosomes. It may act by forming ring-like structures around microtubules, or by serving as a cross-linker or scaffold at the attachment site [].

>PF14931 IFT20: Intraflagellar transport complex B, subunit 20

Probab=83.22  E-value=18  Score=27.38  Aligned_cols=61  Identities=20%  Similarity=0.379  Sum_probs=35.5

Q ss_pred             hHHHHHHHHHHHHHHH--HHHHH--hhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           15 ILSDVVRMMEQLRTEA--QKLKQ--STEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        15 IL~DAir~lkqLr~e~--~~Lk~--~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |++.-+.++.++-.++  +|||+  .-..|.+..+.=..++..|.......+.|.|||..|+.++
T Consensus        42 iv~~~~~~~~~~A~~VE~eKlkAIG~RN~l~s~~k~R~~~~q~lq~~I~Ek~~eLERl~~E~~sL  106 (120)
T PF14931_consen   42 IVKGFIEILDELAKRVENEKLKAIGARNLLKSEAKQREAQQQQLQALIAEKKMELERLRSEYESL  106 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555666666654443  45554  3334445555555666666666666667777777766653

>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal

Probab=83.19  E-value=6.6  Score=28.34  Aligned_cols=40  Identities=20%  Similarity=0.378  Sum_probs=16.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNEL   54 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnEL   54 (136)
                      |.-|--.++.+|..+++.+......|+....+|..+-.++
T Consensus        61 v~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~  100 (110)
T TIGR02338        61 VKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLKEL  100 (110)
T ss_pred             heecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333334444444444444444444444444443333333

Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.

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

Probab=83.16  E-value=7.3  Score=30.46  Aligned_cols=42  Identities=29%  Similarity=0.484  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKAD   64 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~e   64 (136)
                      +..|..++++|++....|++.+.+|.....+++.+.+.+-.+
T Consensus        96 ie~l~k~~~~l~~~~~~l~~~l~~l~~~~~~l~~~~q~~~q~  137 (145)
T COG1730          96 IEFLKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQQLQQK  137 (145)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344567889999999999999999999988888887766543

>PRK04863 mukB cell division protein MukB; Provisional

Probab=83.15  E-value=6.1  Score=40.66  Aligned_cols=64  Identities=19%  Similarity=0.292  Sum_probs=55.2

Q ss_pred             chhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           11 DKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        11 DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |=..+|++.-.+.-.|+.++++++++...+.+..+....+.+....+...+++.+..++++++.
T Consensus       975 ~~~~~l~~~~~~~~~Le~~Le~iE~~~~~areql~qaq~q~~q~~q~l~slksslq~~~e~L~E 1038 (1486)
T PRK04863        975 DAAEMLAKNSDLNEKLRQRLEQAEQERTRAREQLRQAQAQLAQYNQVLASLKSSYDAKRQMLQE 1038 (1486)
T ss_pred             HHHhHhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3457899999999999999999999999999999999999999988888888877777666655

>PF03954 Lectin_N: Hepatic lectin, N-terminal domain; InterPro: IPR005640 Animal lectins display a wide variety of architectures

Probab=83.00  E-value=3.6  Score=32.27  Aligned_cols=51  Identities=25%  Similarity=0.414  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHhhH----HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           24 EQLRTEAQKLKQSTE----DLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~----~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+||.|..-||+...    +...|++.|..-=..+.+--..|+++-|+-++++++
T Consensus        58 ~qlq~dl~tLretfsNFssst~aEvqaL~S~G~sl~~kVtSLea~lEkqqQeLkA  112 (138)
T PF03954_consen   58 SQLQRDLRTLRETFSNFSSSTLAEVQALSSQGGSLQDKVTSLEAKLEKQQQELKA  112 (138)
T ss_pred             HHHHHHHHHHHHHHhcccHHHHHHHHHHHhccccHHhHcccHHHHHHHHHHHHhh
Confidence            589999999999877    566678888888888889999999999999999988

They are classified according to the carbohydrate-recognition domain (CRD) of which there are two main types, S-type and C-type. C-type lectins display a wide range of specificities. They require Ca2+ for their activity They are found predominantly but not exclusively in vertebrates. This entry presents N-terminal domain, which is found in C-type lectins.; GO: 0005529 sugar binding, 0016020 membrane

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]

Probab=82.94  E-value=9.1  Score=37.73  Aligned_cols=15  Identities=27%  Similarity=0.532  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHHhhHH
Q 032660           25 QLRTEAQKLKQSTED   39 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~   39 (136)
                      ++..+++.|+.+.+.
T Consensus       734 ~~~~~~~~l~~~~~~  748 (1163)
T COG1196         734 QLQSRLEELEEELEE  748 (1163)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            333333333333333

>cd07429 Cby_like Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins

Probab=82.88  E-value=3  Score=31.39  Aligned_cols=35  Identities=26%  Similarity=0.255  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL   61 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~L   61 (136)
                      ..+..+||..|..|+||.+.|+-+.+=|.|..+..
T Consensus        71 ~~e~~rlkkk~~~LeEENNlLklKievLLDMLtet  105 (108)
T cd07429          71 GREVLRLKKKNQQLEEENNLLKLKIEVLLDMLAET  105 (108)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35677888888888888888888888787766543

Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif.

>PF09730 BicD: Microtubule-associated protein Bicaudal-D; InterPro: IPR018477 BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER) []

Probab=82.87  E-value=4.8  Score=38.67  Aligned_cols=46  Identities=33%  Similarity=0.505  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHH-------HHHHHHHHHHHHhHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELK-------AEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~-------~EKnELrdEk~~Lk~eke~Le   69 (136)
                      .+|+...+.|..+...|.++++++|       ++-+||.+||-.|+.++..|.
T Consensus        65 ~~~~~~~~~~e~~~~~lr~e~ke~K~rE~rll~dyselEeENislQKqvs~Lk  117 (717)
T PF09730_consen   65 QELRKECEDLELERKRLREEIKEYKFREARLLQDYSELEEENISLQKQVSVLK  117 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence            3444444444444455555555444       345666667766666655554

Glycogen synthase kinase-3beta (GSK-3beta) is required for the binding of BICD to dynein but not to dynactin, acting to maintain the anchoring of microtubules to the centromere []. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells [].; GO: 0006810 transport, 0005794 Golgi apparatus

>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A

Probab=82.87  E-value=9.7  Score=26.22  Aligned_cols=18  Identities=28%  Similarity=0.466  Sum_probs=10.5

Q ss_pred             HHHHhHHHHHHHHHHHHh
Q 032660           57 EKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        57 Ek~~Lk~eke~Le~qlk~   74 (136)
                      .....+...+||..+++.
T Consensus        65 ~~~~~k~~~~KL~~df~~   82 (102)
T PF14523_consen   65 NDRQQKLQREKLSRDFKE   82 (102)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHH
Confidence            334445666677666665

>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein

Probab=82.80  E-value=12  Score=32.79  Aligned_cols=26  Identities=19%  Similarity=0.365  Sum_probs=14.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHH
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDL   40 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L   40 (136)
                      .++++..-+.+|++++.+++.....+
T Consensus       237 ~~~~~~~~i~~l~~~i~~~~~~~~~~  262 (457)
T TIGR01000       237 ILATIQQQIDQLQKSIASYQVQKAGL  262 (457)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            44455555556666665555555543

This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.

>PRK04406 hypothetical protein; Provisional

Probab=82.78  E-value=9.4  Score=26.58  Aligned_cols=40  Identities=13%  Similarity=0.259  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL   61 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~L   61 (136)
                      -|.+|...+.-+...++.|.+.+-....+...|+.+...|
T Consensus        12 Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L   51 (75)
T PRK04406         12 RINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYV   51 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555544444444444444444444

>PLN02678 seryl-tRNA synthetase

Probab=82.78  E-value=8.8  Score=34.70  Aligned_cols=57  Identities=28%  Similarity=0.354  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHH---HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQ---EKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~---ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .+.-+.+||.|.+++-+++..+.   ++..+|..|-++|++|...|+.+...+++++..+
T Consensus        45 l~~~~e~lr~erN~~sk~I~~~k~~~~~~~~l~~~~~~Lk~ei~~le~~~~~~~~~l~~~  104 (448)
T PLN02678         45 RQFELDSLRKEFNKLNKEVAKLKIAKEDATELIAETKELKKEITEKEAEVQEAKAALDAK  104 (448)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34557788888888888776533   4567888888889999999999999999888884

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=82.50  E-value=9  Score=37.02  Aligned_cols=60  Identities=18%  Similarity=0.354  Sum_probs=34.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ||-|-.|++.-.+.|.-+|+.....|+++|.++.....||+.+.-.-+.|.++|+..+.+
T Consensus        80 ~~~e~~RI~~sVs~EL~ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieq  139 (907)
T KOG2264|consen   80 ILREQKRILASVSLELTELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQ  139 (907)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHH
Confidence            355555555555666666666666666666666555555555555555555555555444

>KOG4643 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=82.46  E-value=9.3  Score=38.59  Aligned_cols=62  Identities=16%  Similarity=0.223  Sum_probs=49.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           14 TILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        14 sIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .+|-+++..+..|.+...+||+.+.+.......+...+.+|+.++..|+.|-.-|..||+.+
T Consensus       495 k~L~~r~~elsrl~a~~~elkeQ~kt~~~qye~~~~k~eeLe~~l~~lE~ENa~LlkqI~~L  556 (1195)
T KOG4643|consen  495 KSLNNRDLELSRLHALKNELKEQYKTCDIQYELLSNKLEELEELLGNLEEENAHLLKQIQSL  556 (1195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            57888999999999999999998888888877777777777777777777777776666654

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=82.26  E-value=11  Score=30.15  Aligned_cols=36  Identities=31%  Similarity=0.519  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      .-||.+.+..+..|..|.+++..|+.+-+.|++|..
T Consensus        84 ~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~eL~  119 (182)
T PF15035_consen   84 ALLREQLEQARKANEALQEDLQKLTQDWERLRDELE  119 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346777777777777777777777777666655543

>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species

Probab=82.23  E-value=7.1  Score=31.93  Aligned_cols=49  Identities=24%  Similarity=0.400  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHH-----HHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKE-----LKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~-----L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +....+|.-|.-.+..|+++|..     +..+.|.|.-|...++.+.|-++-+|
T Consensus       108 ~s~~~ei~~L~~kI~~L~~~in~~~k~~~n~~i~slk~EL~d~iKe~e~~emeL  161 (181)
T PF04645_consen  108 KSIKKEIEILRLKISSLQKEINKNKKKDLNEEIESLKSELNDLIKEREIREMEL  161 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555432     33444555555555555555555443

>PF09730 BicD: Microtubule-associated protein Bicaudal-D; InterPro: IPR018477 BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER) []

Probab=82.13  E-value=7.1  Score=37.55  Aligned_cols=19  Identities=32%  Similarity=0.510  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHHhhHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQE   42 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~e   42 (136)
                      |++|.++..-+.+|+.|..
T Consensus        44 k~~~~~~~~~~~e~~rl~~   62 (717)
T PF09730_consen   44 KQLRQELSNVQAENERLSQ   62 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3444433333333333333

Glycogen synthase kinase-3beta (GSK-3beta) is required for the binding of BICD to dynein but not to dynactin, acting to maintain the anchoring of microtubules to the centromere []. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells [].; GO: 0006810 transport, 0005794 Golgi apparatus

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

Probab=82.02  E-value=7.5  Score=26.17  Aligned_cols=46  Identities=15%  Similarity=0.344  Sum_probs=27.9

Q ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           31 QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        31 ~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      .+|..+..++...+..++.|-.+++++...++.-+.+|=.-+..++
T Consensus         3 ~elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ll~lYE~Vs   48 (55)
T PF05377_consen    3 DELENELPRIESSINTVKKENEEISESVEKIEENVKDLLSLYEVVS   48 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555555666666666666777767666666655555543

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) [].

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

Probab=81.95  E-value=8.7  Score=32.21  Aligned_cols=55  Identities=20%  Similarity=0.384  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      |....+.-..-+|.+..+=.....+......+|..||..|+.+++.|++|+..+.
T Consensus       195 y~err~rNN~A~~kSR~~~k~~~~e~~~r~~~leken~~lr~~v~~l~~el~~~~  249 (269)
T KOG3119|consen  195 YKERRRRNNEAVRKSRDKRKQKEDEMAHRVAELEKENEALRTQVEQLKKELATLR  249 (269)
T ss_pred             HHHHHHhhhHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333344444444444445567777778888888888888888888877753

>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=81.91  E-value=12  Score=25.40  Aligned_cols=45  Identities=11%  Similarity=0.314  Sum_probs=33.6

Q ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           31 QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        31 ~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |.+.++.....+.+..++....|-...+..|..++++|+.++..+
T Consensus        14 Q~~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee~   58 (61)
T PF08826_consen   14 QAIQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEMEEL   58 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            456667777777777777777777888888888888888877653

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

>PF08286 Spc24: Spc24 subunit of Ndc80; InterPro: IPR013252 Spc24 is a component of the evolutionarily conserved kinetochore-associated Ndc80 complex and is involved in chromosome segregation []

Probab=81.83  E-value=0.44  Score=34.96  Aligned_cols=43  Identities=28%  Similarity=0.418  Sum_probs=0.9

Q ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           32 KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +|..+.-++-.++..|..+-+.|+.|...|+.+.+.|+.|...
T Consensus         3 ~Ld~~k~~laK~~~~LE~~l~~l~~el~~L~~~l~eLe~~~~~   45 (118)
T PF08286_consen    3 ELDNEKFRLAKELSDLESELESLQSELEELKEELEELEEQEVE   45 (118)
T ss_dssp             ----------------------------------------HT-
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            4444444444444555555555555555555555555555443

; PDB: 2VE7_D 2FV4_B 2FTX_B.

>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5

Probab=81.80  E-value=5.4  Score=28.82  Aligned_cols=38  Identities=39%  Similarity=0.448  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL   61 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~L   61 (136)
                      .+|..+.+.|+++.+.|+..+..|....++++.=+..|
T Consensus         2 qql~~q~~ql~~~i~~l~~~i~~l~~~i~e~~~~~~~L   39 (126)
T TIGR00293         2 QQLAAELQILQQQVESLQAQIAALRALIAELETAIETL   39 (126)
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46778888888888888888888888887776665444

This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.

>TIGR00634 recN DNA repair protein RecN

Probab=81.72  E-value=5.8  Score=35.86  Aligned_cols=41  Identities=15%  Similarity=0.176  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKAD   64 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~e   64 (136)
                      ++|+.+.+++..+...++.++++++.+.+++..+...|+.+
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~L~~l~~~~~~~~~eld~L~~q  197 (563)
T TIGR00634       157 NEKVKAYRELYQAWLKARQQLKDRQQKEQELAQRLDFLQFQ  197 (563)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            34444444444444444444444444444444444444333

All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.

>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes []

Probab=81.54  E-value=14  Score=24.96  Aligned_cols=45  Identities=13%  Similarity=0.396  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .+++.++.+++.....+++.+..|+       .....++.++.+++.+|..+
T Consensus         2 ~~i~e~l~~ie~~l~~~~~~i~~lE-------~~~~~~e~~i~~~~~~l~~I   46 (71)
T PF10779_consen    2 QDIKEKLNRIETKLDNHEERIDKLE-------KRDAANEKDIKNLNKQLEKI   46 (71)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555555444444443       44445555555666555554

>PRK09973 putative outer membrane lipoprotein; Provisional

Probab=81.36  E-value=11  Score=27.32  Aligned_cols=40  Identities=23%  Similarity=0.390  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      |.+|.++++.|+.....++.+++.++..-..-.+|=.+--
T Consensus        26 vdqLss~V~~L~~kvdql~~dv~~a~aaa~aAk~EA~RAN   65 (85)
T PRK09973         26 VNQLASNVQTLNAKIARLEQDMKALRPQIYAAKSEANRAN   65 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5677777777777777777777766665554444444333

>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans

Probab=81.30  E-value=8.7  Score=34.45  Aligned_cols=27  Identities=22%  Similarity=0.530  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHH
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQE   42 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~e   42 (136)
                      +...-.-|++++.....|..++++|.+
T Consensus       214 l~~~~~el~eik~~~~~L~~~~e~Lk~  240 (395)
T PF10267_consen  214 LQKILEELREIKESQSRLEESIEKLKE  240 (395)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333334455555555555555555555

Its function is unknown.

>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily

Probab=81.29  E-value=9.8  Score=33.22  Aligned_cols=10  Identities=20%  Similarity=0.547  Sum_probs=6.8

Q ss_pred             CccccccCCC
Q 032660          111 GVAMWQFMPP  120 (136)
Q Consensus       111 g~~mWq~~pp  120 (136)
                      |.|++-.+|-
T Consensus       453 glpvLg~iP~  462 (498)
T TIGR03007       453 GLPVLGVIPM  462 (498)
T ss_pred             CCCeEEecCC
Confidence            6677776665

Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene.

>PF15458 NTR2: Nineteen complex-related protein 2

Probab=81.29  E-value=8.1  Score=32.11  Aligned_cols=43  Identities=21%  Similarity=0.470  Sum_probs=21.5

Q ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           31 QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        31 ~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      .+|+.....|+.+...+.....+|+.|+..|...+..|+..|+
T Consensus       211 ~rL~~~l~~le~~~~~~~~~l~~l~~E~~~I~~re~elq~~l~  253 (254)
T PF15458_consen  211 ERLRESLSSLEDSKSQLQQQLESLEKEKEEIEEREKELQELLK  253 (254)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4444444444444444444444555555555555555555553

>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=81.26  E-value=0.76  Score=33.02  Aligned_cols=43  Identities=30%  Similarity=0.468  Sum_probs=15.9

Q ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           30 AQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        30 ~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +..|-.++..|..++.+|+.+.++|+++...++...+.|++.|
T Consensus        27 l~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~~~l   69 (131)
T PF05103_consen   27 LDELAEELERLQRENAELKEEIEELQAQLEELREEEESLQRAL   69 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCCCCT---------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHhh
Confidence            4455555555555555555555555555555555555555544

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.

>PRK14127 cell division protein GpsB; Provisional

Probab=81.22  E-value=5.2  Score=29.99  Aligned_cols=38  Identities=21%  Similarity=0.413  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      +|.++-.+.+.|-++|..|++++..|+.+..+++.+..
T Consensus        31 FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~   68 (109)
T PRK14127         31 FLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQVS   68 (109)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            44444444455555555555555555444444444443

>PF12999 PRKCSH-like: Glucosidase II beta subunit-like

Probab=81.22  E-value=9.8  Score=30.77  Aligned_cols=59  Identities=24%  Similarity=0.285  Sum_probs=33.9

Q ss_pred             chhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           11 DKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        11 DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      ++-..|+.+.|-.  +..+.+..++-....++-+.+-+..+.+++.+...|+.++...+++
T Consensus       117 N~C~e~~~~~~~~--~~~~~~~~~~G~~~r~~~i~~a~~~~~e~~~~l~~l~~ei~~~~~e  175 (176)
T PF12999_consen  117 NTCAELGKEYREE--LEEEEEIYKEGLKIRQELIEEAKKKREELEKKLEELEKEIQAAKQE  175 (176)
T ss_pred             cHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4455555544433  3344444455555555556666666777777777777777666553

>PF08647 BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR013956 BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions []

Probab=81.12  E-value=17  Score=25.88  Aligned_cols=49  Identities=33%  Similarity=0.389  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |.+|+.++......+.+....+..+-.-|.+.+.+|..||.+=.+++.+
T Consensus         1 L~~EL~~~~~a~~~~~~~~~~k~~~~~~lE~k~~rl~~Ek~kadqkyfa   49 (96)
T PF08647_consen    1 LQTELVSMEQAFKELSEQADKKVKELTILEQKKLRLEAEKAKADQKYFA   49 (96)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456666666666666666666666666666666666666666666554

>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]

Probab=81.12  E-value=3.5  Score=39.00  Aligned_cols=48  Identities=23%  Similarity=0.373  Sum_probs=39.8

Q ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCCCCC
Q 032660           34 KQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGF   81 (136)
Q Consensus        34 k~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~~p~f   81 (136)
                      |+-...|+..+++|-.|...||.|+..||.+++.|+.+=+.+.++.+|
T Consensus       301 KEy~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~En~~~kvpsp~  348 (655)
T KOG4343|consen  301 KEYMLGLEARLQALLSENEQLKKENATLKRQLDELVSENQRLKVPSPK  348 (655)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCcccccCCCc
Confidence            445568899999999999999999999999999999877766655443

>PF14988 DUF4515: Domain of unknown function (DUF4515)

Probab=81.01  E-value=13  Score=30.26  Aligned_cols=47  Identities=28%  Similarity=0.451  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      -..+..|-.+|..+...|..+.+.|...+..|++.|+.|+.|..=++
T Consensus       158 ~~~i~~EN~~L~k~L~~l~~e~~~L~~~~~~Le~qk~~L~~eq~~~e  204 (206)
T PF14988_consen  158 TRSIKRENQQLRKELLQLIQEAQKLEARKSQLEKQKQQLQQEQWYLE  204 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            35677888889999999999999999999999999999988876554

>PF13514 AAA_27: AAA domain

Probab=80.99  E-value=13  Score=36.40  Aligned_cols=64  Identities=23%  Similarity=0.416  Sum_probs=49.9

Q ss_pred             chhhhHHHHHHHHHHHHHHHHHHHHh---hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           11 DKATILSDVVRMMEQLRTEAQKLKQS---TEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        11 DKAsIL~DAir~lkqLr~e~~~Lk~~---n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ++-..|..++.-+++++.++++....   +..+..+...+..+.++|+.+...|+.+..+|+...+.
T Consensus       147 g~~~~in~~l~~l~e~~~~l~~~~~~~~~y~~l~~~~~~~~~~~~~l~~~~~~l~~~~~~ler~~~~  213 (1111)
T PF13514_consen  147 GRKPEINQALKELKELERELREAEVRAAEYQELQQALEEAEEELEELRAELKELRAELRRLERLRRA  213 (1111)
T ss_pred             CCChHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67778999999999999999888764   45566667777778888888888888887777765444

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

Probab=80.96  E-value=7.1  Score=34.33  Aligned_cols=61  Identities=15%  Similarity=0.317  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc-cCCCCCCCC
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM-SAPSGFLPH   84 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~-~~~p~f~ph   84 (136)
                      |=|++-|+....+..++......++.+-++|-....+-|.|.|++.+.|.++ ++.|.||-.
T Consensus       108 kvlk~aIq~i~~~~q~~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRle~LqsiRP~~MdE  169 (338)
T KOG3647|consen  108 KVLKSAIQAIQVRLQSSRAQLNNVASDEAALGSKIERRKAELERTRKRLEALQSIRPAHMDE  169 (338)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHH
Confidence            3345555555555566666666677777777777777777777777777776 446666654

>PF04822 Takusan: Takusan; InterPro: IPR006907 This family includes several uncharacterised muridae (mouse and rat) proteins

Probab=80.95  E-value=3.2  Score=29.81  Aligned_cols=25  Identities=32%  Similarity=0.489  Sum_probs=21.6

Q ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHH
Q 032660           35 QSTEDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        35 ~~n~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      ++.+.|.-+++-++.|+||||+-..
T Consensus        19 k~lE~L~~eL~~it~ERnELr~~L~   43 (84)
T PF04822_consen   19 KELERLKFELQKITKERNELRDILA   43 (84)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5667888889999999999999876

>PRK14161 heat shock protein GrpE; Provisional

Probab=80.93  E-value=5.8  Score=31.70  Aligned_cols=41  Identities=27%  Similarity=0.319  Sum_probs=19.7

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 032660           13 ATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNE   53 (136)
Q Consensus        13 AsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnE   53 (136)
                      -+|+.=+-..|.-++.++++|+++.+.|.+....+.+|-.-
T Consensus        11 ~~~~~~~~~~~~~~~~ei~~l~~e~~elkd~~lR~~AefeN   51 (178)
T PRK14161         11 QTINDIAEEIVETANPEITALKAEIEELKDKLIRTTAEIDN   51 (178)
T ss_pred             HHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444445555555555555555444444444333

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

Probab=80.86  E-value=11  Score=31.33  Aligned_cols=31  Identities=23%  Similarity=0.295  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELK   48 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~   48 (136)
                      |--.++..|.++.+..+....+|.+.+...+
T Consensus        78 ~~ks~~qeLe~~L~~~~qk~~tl~e~~en~K  108 (203)
T KOG3433|consen   78 DRKSVLQELESQLATGSQKKATLGESIENRK  108 (203)
T ss_pred             HHHHHHHHHHHHHHHhhhhHhHHHHHHHHHH
Confidence            3344667777777777777777776654333

>TIGR02680 conserved hypothetical protein TIGR02680

Probab=80.86  E-value=11  Score=38.06  Aligned_cols=40  Identities=20%  Similarity=0.413  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      +.+++.+++...++...+++++..|+.++.+|+.+...|+
T Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~le~~~~~l~~~~~~l~  324 (1353)
T TIGR02680       285 LGRARDELETAREEERELDARTEALEREADALRTRLEALQ  324 (1353)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3344444444444444444444444444444444444433

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length.

>PRK13923 putative spore coat protein regulator protein YlbO; Provisional

Probab=80.78  E-value=15  Score=29.68  Aligned_cols=22  Identities=32%  Similarity=0.377  Sum_probs=8.2

Q ss_pred             HHHHHHHhhHHHHHHHHHHHHH
Q 032660           29 EAQKLKQSTEDLQEKIKELKAE   50 (136)
Q Consensus        29 e~~~Lk~~n~~L~ee~~~L~~E   50 (136)
                      ++.+|...|+.|+.+.+.|+.+
T Consensus       112 e~~kl~~~~e~L~~e~~~L~~~  133 (170)
T PRK13923        112 QIGKLQEEEEKLSWENQTLKQE  133 (170)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333

>PF09755 DUF2046: Uncharacterized conserved protein H4 (DUF2046); InterPro: IPR019152 This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain

Probab=80.67  E-value=18  Score=31.76  Aligned_cols=9  Identities=44%  Similarity=0.671  Sum_probs=3.5

Q ss_pred             HHHHHHHHH
Q 032660           44 IKELKAEKN   52 (136)
Q Consensus        44 ~~~L~~EKn   52 (136)
                      |..|..|+.
T Consensus       144 i~~Le~e~~  152 (310)
T PF09755_consen  144 IERLEKEKS  152 (310)
T ss_pred             HHHHHHHHH
Confidence            334433333

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=80.57  E-value=15  Score=33.58  Aligned_cols=59  Identities=15%  Similarity=0.379  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .++...-+.+|..++..++++...+.+.+..|..+-.+.|+.-..++..+..+...++.
T Consensus       378 ysel~e~leel~e~leeie~eq~ei~e~l~~Lrk~E~eAr~kL~~~~~~L~~ikr~l~k  436 (569)
T PRK04778        378 YSELQEELEEILKQLEEIEKEQEKLSEMLQGLRKDELEAREKLERYRNKLHEIKRYLEK  436 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555555555555555555555555555555555555555555555555555544

>PF08738 Gon7: Gon7 family; InterPro: IPR014849 In Saccharomyces cerevisiae Gon7 is a member of the KEOPS protein complex

Probab=80.47  E-value=8.9  Score=28.54  Aligned_cols=39  Identities=26%  Similarity=0.394  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHHHHhhH-HHHHHHHHHHHHHHHHHHHHH
Q 032660           21 RMMEQLRTEAQKLKQSTE-DLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~-~L~ee~~~L~~EKnELrdEk~   59 (136)
                      .+|.+||.++-.|.+.+. -|.++.++-|..+....+++.
T Consensus        54 t~L~~LR~~lt~lQddIN~fLTeRMe~dK~~~~~~~~~~~   93 (103)
T PF08738_consen   54 TYLSELRAQLTTLQDDINEFLTERMEEDKARDAQAGEEKS   93 (103)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccchhhh
Confidence            788899999988887644 677777776666666555544

A protein complex proposed to be involved in transcription and promoting telomere uncapping and telomere elongation [].

>PF12711 Kinesin-relat_1: Kinesin motor; InterPro: IPR024658 Kinesin [, , ] is a microtubule-associated force-producing protein that may play a role in organelle transport

Probab=80.45  E-value=9.4  Score=27.66  Aligned_cols=11  Identities=45%  Similarity=0.652  Sum_probs=4.2

Q ss_pred             HHHHHHHHHHh
Q 032660           51 KNELRDEKQRL   61 (136)
Q Consensus        51 KnELrdEk~~L   61 (136)
                      -..||+|+.+|
T Consensus        53 N~rL~ee~rrl   63 (86)
T PF12711_consen   53 NIRLREELRRL   63 (86)
T ss_pred             HHHHHHHHHHH
Confidence            33344443333

The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds. The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyse ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerisation; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles. A number of proteins have been recently found that contain a domain similar to that of the kinesin 'motor' domain [, ]: Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end. Homo sapiens CENP-E []. CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation. H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end. Saccharomyces cerevisiae KAR3 protein, which is essential for nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis. S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles. Emericella nidulans (Aspergillus nidulans) bimC, which plays an important role in nuclear division. A. nidulans klpA. Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation. C. elegans osm-3. Xenopus laevis Eg5, which may be involved in mitosis. Arabidopsis thaliana KatA, KatB and katC. Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella. C. elegans hypothetical protein T09A5.2. Kinesin-like proteins KLP2 (or KIF15) also contain a kinesin 'motor' domain. They are involved in mitotic spindle assembly, playing a role in positioning spindle poles during mitosis, specifically at prometaphase []. This entry represents a domain of unknown function found in this type of kinesin-like proteins.

>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]

Probab=80.29  E-value=6.2  Score=27.46  Aligned_cols=36  Identities=28%  Similarity=0.355  Sum_probs=20.5

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Q 032660           12 KATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKN   52 (136)
Q Consensus        12 KAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKn   52 (136)
                      -.-|..|+..++.     +.+|.+.+.-|++||.-|++|.+
T Consensus        14 ~~~i~~d~Lslls-----V~El~eRIalLq~EIeRlkAe~~   49 (65)
T COG5509          14 GHEIGNDALSLLS-----VAELEERIALLQAEIERLKAELA   49 (65)
T ss_pred             ccccchhHHHHhh-----HHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456677755543     45555566666666665555544

>COG2841 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.25  E-value=10  Score=26.98  Aligned_cols=51  Identities=20%  Similarity=0.388  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH--------HHHHHHHHHHHhHHHHHHH
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKA--------EKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~--------EKnELrdEk~~Lk~eke~L   68 (136)
                      |.|..||.=-+--.+|=+++..|-..|+....        |-..|+.+|..||-||..+
T Consensus         7 ~~is~Lk~~dahF~rLfd~hn~LDd~I~~~E~n~~~~s~~ev~~LKKqkL~LKDEi~~~   65 (72)
T COG2841           7 DLISKLKANDAHFARLFDKHNELDDRIKRAEGNRQPGSDAEVSNLKKQKLQLKDEIASI   65 (72)
T ss_pred             HHHHHHhccchHHHHHHHHHhHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhHHHHHHH
Confidence            34444444344445555555666666665543        6666777777777666544

>PF02050 FliJ: Flagellar FliJ protein; InterPro: IPR012823 Many flagellar proteins are exported by a flagellum-specific export pathway

Probab=80.23  E-value=15  Score=24.66  Aligned_cols=25  Identities=12%  Similarity=0.368  Sum_probs=10.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHH
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDL   40 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L   40 (136)
                      |+.+.+-+.+...++..|......+
T Consensus         7 l~~~~~~~~~~~~~l~~L~~~~~~~   31 (123)
T PF02050_consen    7 LAEAQQELQEAEEQLEQLQQERQEY   31 (123)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444443

Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects []. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export. The sequences of fliH, fliI and the adjacent gene, fliJ, have been deduced. FliJ was shown to encode a protein of molecular mass 17,302 Da []. It is a membrane-associated protein that affects chemotactic events, mutations in FliJ result in failure to respond to chemotactic stimuli.; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 bacterial-type flagellum, 0016020 membrane, 0044461 bacterial-type flagellum part; PDB: 3AJW_A.

>PF04849 HAP1_N: HAP1 N-terminal conserved region; InterPro: IPR006933 This family is defined by an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues

Probab=80.14  E-value=13  Score=32.45  Aligned_cols=37  Identities=38%  Similarity=0.621  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           38 EDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.|+++++.|..|-+.||.|-+.|+.+....|.+-+.
T Consensus       163 e~Lq~Klk~LEeEN~~LR~Ea~~L~~et~~~EekEqq  199 (306)
T PF04849_consen  163 EALQEKLKSLEEENEQLRSEASQLKTETDTYEEKEQQ  199 (306)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHHhhccHHHHH
Confidence            5677777777777777777777777777666655433

HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntingtons disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34 [].

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

Probab=80.12  E-value=16  Score=30.41  Aligned_cols=49  Identities=20%  Similarity=0.295  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      +=...|+..++..|..++.-++...+|+.+.|-|+++-..|+.|..+++
T Consensus        95 qk~~tl~e~~en~K~~~e~tEer~~el~kklnslkk~~e~lr~el~k~~  143 (203)
T KOG3433|consen   95 QKKATLGESIENRKAGREETEERTDELTKKLNSLKKILESLRWELAKIQ  143 (203)
T ss_pred             hhHhHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3344455566666666666666667888888888887777777777765

>PRK04863 mukB cell division protein MukB; Provisional

Probab=80.10  E-value=12  Score=38.49  Aligned_cols=42  Identities=19%  Similarity=0.270  Sum_probs=16.8

Q ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           33 LKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        33 Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.++...++++++.|+.+.+++..+...++++...+++++..
T Consensus       381 leeEleelEeeLeeLqeqLaelqqel~elQ~el~q~qq~i~~  422 (1486)
T PRK04863        381 NEARAEAAEEEVDELKSQLADYQQALDVQQTRAIQYQQAVQA  422 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333444444444444444444444444444333

>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]

Probab=80.09  E-value=8.2  Score=36.32  Aligned_cols=59  Identities=19%  Similarity=0.296  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH----HHhHHHHHHHHHHHHhccC
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEK----QRLKADKEKLEQQVKAMSA   77 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk----~~Lk~eke~Le~qlk~~~~   77 (136)
                      |-+++--++++.+   +|...++.++.+.-+.-.+.+++++++    .+-+.|+|+||.+|..++.
T Consensus       485 Lee~i~~~~~~i~---El~~~l~~~e~~L~~a~s~~~~~ke~~e~e~~a~~~E~eklE~el~~lnL  547 (622)
T COG5185         485 LEEDIKNLKHDIN---ELTQILEKLELELSEANSKFELSKEENERELVAQRIEIEKLEKELNDLNL  547 (622)
T ss_pred             HHHHhhhHHhHHH---HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhh
Confidence            6666655555544   455667777777766667777777654    4667899999999998764

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

Probab=80.03  E-value=17  Score=26.05  Aligned_cols=30  Identities=30%  Similarity=0.356  Sum_probs=12.1

Q ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 032660           30 AQKLKQSTEDLQEKIKELKAEKNELRDEKQ   59 (136)
Q Consensus        30 ~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~   59 (136)
                      ...|+.....-++||..|+.=-..||.+..
T Consensus         7 Nk~L~~kL~~K~eEI~rLn~lv~sLR~KLi   36 (76)
T PF11544_consen    7 NKELKKKLNDKQEEIDRLNILVGSLRGKLI   36 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333344444444444444444444333

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.

>PF07047 OPA3: Optic atrophy 3 protein (OPA3); InterPro: IPR010754 OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans

Probab=80.01  E-value=17  Score=27.45  Aligned_cols=9  Identities=11%  Similarity=0.342  Sum_probs=4.7

Q ss_pred             hhHHHHHHH
Q 032660           14 TILSDVVRM   22 (136)
Q Consensus        14 sIL~DAir~   22 (136)
                      .+|||++-+
T Consensus        77 ell~E~fiF   85 (134)
T PF07047_consen   77 ELLGEAFIF   85 (134)
T ss_pred             HHHHHHHHH
Confidence            456665543

This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity []. This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.

---

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	136
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	8e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	5e-04
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	3e-05
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	7e-05
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	2e-04
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-04
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	4e-04
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	6e-04

>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 = 44.8 bits (106), Expect = 2e-06
 Identities = 12/62 (19%), Positives = 30/62 (48%)

Query: 16   LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 75
            L++     + L     K +    +L+ ++K+ +  + EL   K++L+ +   L +Q+  +
Sbjct: 1020 LAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAEL 1079

Query: 76   SA 77
             A
Sbjct: 1080 QA 1081

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 43.7 bits (103), Expect = 4e-06
 Identities = 16/55 (29%), Positives = 32/55 (58%)

Query: 21  RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 75
              +QL+ E +K++Q   DL+E+++E +A + +L+ EK       +K+E  +  M
Sbjct: 941 ERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIM 995

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 11/67 (16%), Positives = 27/67 (40%)

Query: 9    KTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL 68
            K      +  +   +  +  +  KL +  + L+E++ +L     E  ++ + L   K K 
Sbjct: 978  KVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKH 1037

Query: 69   EQQVKAM 75
            E  +  +
Sbjct: 1038 ESMISEL 1044

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 12/61 (19%), Positives = 31/61 (50%)

Query: 16   LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 75
            L+     ++      +       +  +KI+EL++  ++L+++ +  KA + K E+Q + +
Sbjct: 1090 LAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDL 1149

Query: 76   S 76
            S
Sbjct: 1150 S 1150

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.0 bits (96), Expect = 4e-05
 Identities = 14/67 (20%), Positives = 37/67 (55%)

Query: 9   KTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL 68
           K +   IL ++   +E+    +Q+L+   + +Q+++ +L+ +  E    +Q+L+ +K   
Sbjct: 922 KQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTA 981

Query: 69  EQQVKAM 75
           + ++K M
Sbjct: 982 DGKIKKM 988

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 11/58 (18%), Positives = 24/58 (41%)

Query: 16   LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 73
            +SD+   +E  +    K ++   DL E+++ LK E  +  D     +  +    +   
Sbjct: 1125 ISDLQEDLESEKAARNKAEKQKRDLSEELEALKTELEDTLDTTATQQELRGSDYKDDD 1182

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 40.2 bits (94), Expect = 7e-05
 Identities = 14/69 (20%), Positives = 33/69 (47%)

Query: 9    KTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL 68
            K      + D+   +E+     QKL+        KIK+++ +   + D+  +L  +++ L
Sbjct: 950  KKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLL 1009

Query: 69   EQQVKAMSA 77
            E++V  ++ 
Sbjct: 1010 EERVSDLTT 1018

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 7/54 (12%), Positives = 25/54 (46%)

Query: 23   MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS 76
            +E   ++     +   +L+  I +L+ +    +  + + +  K  L ++++A+ 
Sbjct: 1104 LEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDLSEELEALK 1157

>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 = 37.9 bits (88), Expect = 5e-04
 Identities = 13/58 (22%), Positives = 31/58 (53%)

Query: 16   LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK 73
            L    +  ++L    +KL+  + DL E+I EL+A+  EL+ +  + + + +    +++
Sbjct: 1048 LKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLE 1105

>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 = 37.1 bits (86), Expect = 9e-04
 Identities = 15/67 (22%), Positives = 33/67 (49%)

Query: 9   KTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL 68
           K      L     +  +      +L    ++L+E + E++A   E  +  Q+L+A+K+K+
Sbjct: 894 KNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKM 953

Query: 69  EQQVKAM 75
           +QQ+  +
Sbjct: 954 QQQMLDL 960

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 3/60 (5%)

Query: 21  RMMEQLRTEA---QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSA 77
           R +++L+ EA   ++ K+    L+ KI +L+ + +E   E + L      LE      + 
Sbjct: 904 RELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETE 963

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 13/58 (22%), Positives = 31/58 (53%), Gaps = 4/58 (6%)

Query: 23   MEQLRTEAQKLKQSTEDLQEKIKELKAE----KNELRDEKQRLKADKEKLEQQVKAMS 76
            + +LR E  + +   + ++E   + K E     +EL+++   LK +KE+L +++   +
Sbjct: 993  IAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQA 1050

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 40.1 bits (94), Expect = 8e-05
 Identities = 6/62 (9%), Positives = 22/62 (35%)

Query: 16  LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM 75
           + +  +  + L  +   L+ +     EK++          +E +        L++++  +
Sbjct: 937 IDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKL 996

Query: 76  SA 77
             
Sbjct: 997 RK 998

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 7/65 (10%), Positives = 24/65 (36%)

Query: 11  DKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ 70
            +A  +    ++   L  +  +L++  ++  ++ K L  + N L               +
Sbjct: 911 IEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVE 970

Query: 71  QVKAM 75
           +++  
Sbjct: 971 RLRMS 975

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 9   KTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEK--NELRDEKQR---LKA 63
           +  K+ I+   VR     R    +  ++   LQ   + + A++   +L+ E +     K 
Sbjct: 863 REHKSIIIQKHVRGWLA-RVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKK 921

Query: 64  DKEKLEQQVKAM 75
               LE ++  +
Sbjct: 922 LHIGLENKIMQL 933

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 37.8 bits (88), Expect = 5e-04
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 22   MMEQLRTEAQKLKQSTEDLQEKIKELKA---EKNELRDEKQRLKADKEKLEQQVKAM 75
            +     TE +KL+   E L+   +E K        L++E  +L+ +  + + + K +
Sbjct: 954  LEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTI 1010

>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 = 39.2 bits (92), Expect = 3e-05
 Identities = 12/50 (24%), Positives = 23/50 (46%)

Query: 6  RPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR 55
             K  K  IL      +  ++ E QKL    + L+++ ++LK +  +L 
Sbjct: 37 NNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQLG 86

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B Length = 83

 Score = 38.1 bits (89), Expect = 7e-05
 Identities = 10/50 (20%), Positives = 22/50 (44%)

Query: 6  RPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR 55
          +  K  +A IL      ++ +R +    +Q  +DL+ +   L+ +   L 
Sbjct: 32 QGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRALG 81

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A Length = 62

 Score = 36.6 bits (85), Expect = 2e-04
 Identities = 13/44 (29%), Positives = 24/44 (54%)

Query: 31 QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 74
          ++  +    L+EK+K LKA+ +EL      L+    +L+Q+V  
Sbjct: 18 KRKLERIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKVMN 61

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 37.8 bits (87), Expect = 3e-04
 Identities = 9/51 (17%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 20  VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ 70
           +   ++L  E + +++  E+ +++++E     +++ +++ R KA K+  E 
Sbjct: 74  IAQADRLTQEPESIRKWREEQRKRLQE-LDAASKVMEQEWREKAKKDLEEW 123

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1 Length = 61

 Score = 35.8 bits (83), Expect = 4e-04
 Identities = 12/44 (27%), Positives = 25/44 (56%)

Query: 31 QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA 74
          QK K   + L++K ++L +   +L+ E   L+ +  +L+Q + A
Sbjct: 18 QKRKVWVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLKQLLLA 61

>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 = 35.8 bits (83), Expect = 6e-04
 Identities = 13/48 (27%), Positives = 23/48 (47%)

Query: 4  PGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEK 51
           G   K +K+ +L   +  +  L+   QKLKQ    L+  + + K+ K
Sbjct: 33 VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSKSLK 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	136
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	98.76
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	98.49
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	98.43
4ati_A	118	MITF, microphthalmia-associated transcription fact	98.18
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	98.14
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	97.99
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	97.97
4h10_B	71	Circadian locomoter output cycles protein kaput; B	97.54
4ath_A	83	MITF, microphthalmia-associated transcription fact	97.26
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	97.13
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	96.91
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	96.63
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	96.29
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	96.25
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	96.19
3he5_B	52	Synzip2; heterodimeric coiled-coil, de novo protei	96.0
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	95.96
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	95.86
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	95.61
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	95.58
1a0a_A	63	BHLH, protein (phosphate system positive regulator	95.47
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	95.23
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	95.2
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	94.91
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	94.83
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	94.81
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	94.79
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	94.75
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	94.75
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	94.74
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	94.7
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	94.6
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	94.43
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	94.43
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	94.26
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	94.25
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	94.22
2oqq_A	42	Transcription factor HY5; homodimer leucine zipper	94.14
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	94.13
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	94.05
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	94.03
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	93.98
3bas_A	89	Myosin heavy chain, striated muscle/general contro	93.96
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	93.88
3cve_A	72	Homer protein homolog 1; coiled coil, alternative	93.87
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	93.77
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	93.67
3u06_A	412	Protein claret segregational; motor domain, stalk	93.65
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	93.44
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	93.43
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	93.42
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	93.41
1deb_A	54	APC protein, adenomatous polyposis coli protein; c	93.37
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	93.36
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	93.27
3vmx_A	48	Voltage-gated hydrogen channel 1; coiled-coil, ION	93.2
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	93.15
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	93.09
3cvf_A	79	Homer-3, homer protein homolog 3; coiled coil, alt	93.07
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	93.04
2oto_A	155	M protein; helical coiled coil, fibrinogen-binding	92.99
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	92.98
3he5_A	49	Synzip1; heterodimeric coiled-coil, de novo protei	92.98
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	92.89
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	92.84
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	92.83
3htk_A	60	Structural maintenance of chromosomes protein 5; S	92.68
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	92.63
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	92.56
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	92.54
1zhc_A	76	Hypothetical protein HP1242; A-helical protein, un	92.34
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	92.32
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	92.3
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	92.18
2wt7_B	90	Transcription factor MAFB; transcription, transcri	91.94
2oxj_A	34	Hybrid alpha/beta peptide based on the GCN4-P1 Se	91.81
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	91.77
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	91.69
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	91.58
3oa7_A	206	Head morphogenesis protein, chaotic nuclear migra	91.53
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	91.46
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	91.33
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	91.27
1wle_A	501	Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bo	91.22
1gk6_A	59	Vimentin; intermediate filament, dimer, parallel c	91.2
3v86_A	27	De novo design helix; computational design of A pr	91.16
4f3l_A	361	Mclock, circadian locomoter output cycles protein	91.08
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	90.9
2dq0_A	455	Seryl-tRNA synthetase; coiled-coil, homodimer, str	90.8
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	90.78
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	90.74
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	90.69
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	90.68
1wle_A	501	Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bo	90.67
2ocy_A	154	RAB guanine nucleotide exchange factor SEC2; RAB,	90.6
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	90.45
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	90.41
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	90.39
3iv1_A	78	Tumor susceptibility gene 101 protein; coiled_COIL	90.32
3bas_A	89	Myosin heavy chain, striated muscle/general contro	90.22
3qne_A	485	Seryl-tRNA synthetase, cytoplasmic; amino acid bio	90.21
3c3g_A	33	Alpha/beta peptide with the GCN4-PLI SIDE chain S	90.17
3trt_A	77	Vimentin; cytoskeleton, intermediate filament, alp	90.07
3a2a_A	58	Voltage-gated hydrogen channel 1; voltage-gated pr	90.04
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	89.81
2w6a_A	63	ARF GTPase-activating protein GIT1; PIX, zinc, sig	89.79
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	89.76
2j5u_A	255	MREC protein; bacterial cell shape determining pro	89.71
3m48_A	33	General control protein GCN4; leucine zipper, synt	89.55
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	89.48
2no2_A	107	HIP-I, huntingtin-interacting protein 1; clathrin	89.35
1ses_A	421	Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A	89.35
1wt6_A	81	Myotonin-protein kinase; coiled-coil, kinase activ	89.33
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	89.28
1uix_A	71	RHO-associated kinase; coiled-coil, transferase; H	89.23
1l8d_A	112	DNA double-strand break repair RAD50 ATPase; zinc	89.15
3c3f_A	34	Alpha/beta peptide with the GCN4-PLI SIDE chain S	89.08
1x8y_A	86	Lamin A/C; structural protein, intermediate filame	89.06
3htk_A	60	Structural maintenance of chromosomes protein 5; S	89.02
1gk4_A	84	Vimentin; intermediate filament, dimer, parallel c	89.01
2wq1_A	33	General control protein GCN4; TAA, nucleus, coiled	88.85
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	88.76
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	88.43
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	88.16
3swk_A	86	Vimentin; cytoskeleton, intermediate filament, alp	87.79
1kd8_B	36	GABH BLL, GCN4 acid base heterodimer base-D12LA16L	87.59
3iv1_A	78	Tumor susceptibility gene 101 protein; coiled_COIL	87.44
1uii_A	83	Geminin; human, DNA replication, cell cycle; 2.00A	87.37
1wlq_A	83	Geminin; coiled-coil; 2.80A {Mus musculus} PDB: 2z	87.28
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	87.1
3trt_A	77	Vimentin; cytoskeleton, intermediate filament, alp	86.99
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	86.65
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	86.64
2wt7_B	90	Transcription factor MAFB; transcription, transcri	86.55
2xv5_A	74	Lamin-A/C; structural protein, intermediate filame	86.47
2bni_A	34	General control protein GCN4; four helix bundle, a	86.43
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	86.13
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	86.01
1uo4_A	34	General control protein GCN4; four helix bundle, c	85.94
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	85.79
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	85.38
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	85.38
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	85.37
1kd8_A	36	GABH AIV, GCN4 acid base heterodimer acid-D12IA16V	85.17
3w03_C	184	DNA repair protein XRCC4; coiled-coil, NHEJ, DSBS	85.11
1a93_B	34	MAX protein, coiled coil, LZ; leucine zipper, 2D s	85.0
3oa7_A	206	Head morphogenesis protein, chaotic nuclear migra	84.87
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	84.8
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	84.69
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	84.57
2zxx_A	79	Geminin; coiled-coil, cell cycle, coiled coil, DNA	84.56
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	84.56
1gk4_A	84	Vimentin; intermediate filament, dimer, parallel c	84.47
2hy6_A	34	General control protein GCN4; protein design, para	84.41
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	84.39
2zxx_A	79	Geminin; coiled-coil, cell cycle, coiled coil, DNA	84.35
3ibp_A	302	Chromosome partition protein MUKB; structural main	84.29
2ve7_A	315	Kinetochore protein HEC1, kinetochore protein SPC;	84.18
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	84.12
2wg5_A	109	General control protein GCN4, proteasome-activatin	83.87
2zvf_A	171	Alanyl-tRNA synthetase; C-terminal, oligomerizatio	83.85
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	83.85
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	83.83
1s1c_X	71	RHO-associated, coiled-coil containing protein kin	83.71
2dq3_A	425	Seryl-tRNA synthetase; coiled-coil, homodimer, str	83.67
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	83.46
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	83.22
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	83.14
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	83.12
3he4_B	46	Synzip5; heterodimeric coiled-coil, de novo protei	83.08
1l8d_A	112	DNA double-strand break repair RAD50 ATPase; zinc	83.03
3u06_A	412	Protein claret segregational; motor domain, stalk	82.93
4dzn_A	33	Coiled-coil peptide CC-PIL; de novo protein; HET:	82.79
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	82.76
4aj5_1	101	SKA3, spindle and kinetochore-associated protein 3	82.73
3rrk_A	357	V-type ATPase 116 kDa subunit; alpha beta fold, pr	82.71
1dip_A	78	Delta-sleep-inducing peptide immunoreactive peptid	82.48
3m48_A	33	General control protein GCN4; leucine zipper, synt	82.38
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	82.37
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	82.29
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	82.26
1wt6_A	81	Myotonin-protein kinase; coiled-coil, kinase activ	82.08
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	82.06
3lss_A	484	Seryl-tRNA synthetase; aminoacyl-tRNA synthetase,	82.02
3lss_A	484	Seryl-tRNA synthetase; aminoacyl-tRNA synthetase,	81.87
3rrk_A	357	V-type ATPase 116 kDa subunit; alpha beta fold, pr	80.79
3ni0_A	99	Bone marrow stromal antigen 2; coiled-coil, antivi	80.75
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	80.7
3a7o_A	75	Autophagy protein 16; coiled-coil, coiled coil, cy	80.66
2wvr_A	209	Geminin; DNA replication license, DNA replication	80.55
2wvr_A	209	Geminin; DNA replication license, DNA replication	80.52
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	80.48
4aj5_K	123	Spindle and kinetochore-associated protein 2; cell	80.43
3mov_A	95	Lamin-B1; LMNB1, B-type lamins, intermediate filam	80.28
1uii_A	83	Geminin; human, DNA replication, cell cycle; 2.00A	80.11
1kd8_B	36	GABH BLL, GCN4 acid base heterodimer base-D12LA16L	80.07
1kd8_A	36	GABH AIV, GCN4 acid base heterodimer acid-D12IA16V	80.07
2ve7_C	250	Kinetochore protein NUF2, kinetochore protein SPC;	80.06

>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=98.76  E-value=2.1e-08  Score=69.21  Aligned_cols=45  Identities=27%  Similarity=0.402  Sum_probs=40.6

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Q 032660            4 PGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELK   48 (136)
Q Consensus         4 P~rp~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~   48 (136)
                      |+...|+|||+||.+||.||+.|+.+++.|+++++.|+..++..+
T Consensus        33 P~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~~~~~   77 (82)
T 1am9_A           33 VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (82)
T ss_dssp             TCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            555589999999999999999999999999999999999887654

>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=98.49  E-value=2.6e-07  Score=63.13  Aligned_cols=35  Identities=23%  Similarity=0.417  Sum_probs=28.3

Q ss_pred             CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHH
Q 032660            7 PPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQ   41 (136)
Q Consensus         7 p~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~   41 (136)
                      ..|.+|++||.+||.||+.|+.++++|+.+.+.|.
T Consensus        33 ~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~   67 (83)
T 1nkp_B           33 GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   67 (83)
T ss_dssp             TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46999999999999999999998888765433333

>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=98.43  E-value=6.7e-07  Score=62.58  Aligned_cols=47  Identities=26%  Similarity=0.356  Sum_probs=37.2

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNEL   54 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnEL   54 (136)
                      .|.+|++||.+||.||+.|+.+.++|..+.+.|+.+...|..+..+|
T Consensus        39 ~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~~~n~~L~~rl~~L   85 (88)
T 1nkp_A           39 EKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQL   85 (88)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            69999999999999999999998888777666665555555555444

>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A

Probab=98.18  E-value=1e-06  Score=64.58  Aligned_cols=55  Identities=25%  Similarity=0.367  Sum_probs=27.6

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      .|+|||+||.+||.||+.|+.++++|+++..           +...|+.++..|...+..||.|.+
T Consensus        61 ~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~-----------~~~~l~~~n~~L~~riqeLE~~a~  115 (118)
T 4ati_A           61 MRWNKGTILKASVDYIRKLQREQQRAKDLEN-----------RQKKLEHANRHLLLRVQELEMQAR  115 (118)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC-----------------------------------
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4899999999999999999999999987532           233455666666666666666544

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1

Probab=98.14  E-value=6.5e-06  Score=56.81  Aligned_cols=45  Identities=16%  Similarity=0.292  Sum_probs=38.2

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKN   52 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKn   52 (136)
                      .|..|++||..|+.|+++|+.+.++|..+++.|+.++..|..+.+
T Consensus        34 ~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~e~~~L~~~L~   78 (80)
T 1nlw_A           34 SRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLE   78 (80)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            688999999999999999999999888888777777777766544

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=97.99  E-value=6.5e-05  Score=52.87  Aligned_cols=60  Identities=18%  Similarity=0.448  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |-.|+.-+.-|+-|++.||+.|..|.++..++..++..|+.|+..|+.|...-+..|.++
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            456788888899999999999999999999999999999999999999998888777763

>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=97.97  E-value=9.9e-06  Score=55.07  Aligned_cols=36  Identities=22%  Similarity=0.438  Sum_probs=32.7

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEK   43 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee   43 (136)
                      .|.+|++||..||.||+.|+.++++|+.+++.|+.+
T Consensus        44 ~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~~   79 (80)
T 1hlo_A           44 EKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ   79 (80)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHH
T ss_pred             CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            589999999999999999999999999888887754

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=97.54  E-value=7.3e-05  Score=51.04  Aligned_cols=30  Identities=27%  Similarity=0.477  Sum_probs=26.3

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHHHHHHHH
Q 032660            4 PGRPPKTDKATILSDVVRMMEQLRTEAQKL   33 (136)
Q Consensus         4 P~rp~K~DKAsIL~DAir~lkqLr~e~~~L   33 (136)
                      |+...|+||++||.+||.||++|+.++.=|
T Consensus        35 P~~~~K~dK~sIL~~aI~yik~Lq~~~~~~   64 (71)
T 4h10_B           35 PGNARKMDKSTVLQKSIDFLRKHKEITAWL   64 (71)
T ss_dssp             SSCCSCCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHHhhhHH
Confidence            666679999999999999999999987654

>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus}

Probab=97.26  E-value=0.002  Score=45.45  Aligned_cols=56  Identities=25%  Similarity=0.334  Sum_probs=39.2

Q ss_pred             CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660            7 PPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus         7 p~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      -.|..|++||.-|+.|++.|+.+.++++++...+           .-|...+..|.--+-.||-|-+
T Consensus        25 ~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r~-----------k~le~~n~~l~~riqELE~qa~   80 (83)
T 4ath_A           25 DMRWNKGTILKASVDYIRKLQREQQRAKDLENRQ-----------KKLEHANRHLLLRVQELEMQAR   80 (83)
T ss_dssp             TCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHhhhhhHHHHHHHHHHHHHHH
Confidence            3589999999999999999999999988765432           2334444445444555555443

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=97.13  E-value=0.0023  Score=48.02  Aligned_cols=52  Identities=25%  Similarity=0.272  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.++..|+..||.++.+++.++.+++.|..+|++|+..|+.++-+||..+..
T Consensus        84 l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~~~  135 (138)
T 3hnw_A           84 IENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETELND  135 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3344555556777777777777777777777777777777777777777653

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=96.91  E-value=0.008  Score=42.16  Aligned_cols=55  Identities=27%  Similarity=0.406  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHH-------HHHHHHHHHHh
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKA-------DKEKLEQQVKA   74 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~-------eke~Le~qlk~   74 (136)
                      ..++.+|-..|+.+=+.+.-|+.++.+||.+.+.|.+|+..+++       |.++|.++...
T Consensus         5 ~ElleqLE~KIq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~   66 (81)
T 2jee_A            5 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNG   66 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Confidence            36789999999999999999888888888888888888887555       55555555443

>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=96.63  E-value=0.00013  Score=47.53  Aligned_cols=24  Identities=25%  Similarity=0.382  Sum_probs=21.5

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQ   31 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~   31 (136)
                      .|+||++||.+||.||++|+.+.+
T Consensus        41 ~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A           41 SGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             TCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHhc
Confidence            589999999999999999987654

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=96.29  E-value=0.038  Score=41.32  Aligned_cols=51  Identities=14%  Similarity=0.261  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ..|+.+++.+++++..|..+...+..+.++++.|+..|+.++..|+.++..
T Consensus        78 ~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~  128 (138)
T 3hnw_A           78 DSLSLDIENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVK  128 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555555555555566666666666666666666666654

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=96.25  E-value=0.0023  Score=43.46  Aligned_cols=22  Identities=41%  Similarity=0.475  Sum_probs=19.8

Q ss_pred             CCCCchhhhHHHHHHHHHHHHH
Q 032660            7 PPKTDKATILSDVVRMMEQLRT   28 (136)
Q Consensus         7 p~K~DKAsIL~DAir~lkqLr~   28 (136)
                      ..|+|||+||.+||.||+.|+.
T Consensus        42 ~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A           42 SRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             SSCCCHHHHHHHHHHHHHHHSC
T ss_pred             cccccHHHHHHHHHHHHHHHhc
Confidence            3699999999999999999864

>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=96.19  E-value=0.0084  Score=38.62  Aligned_cols=40  Identities=15%  Similarity=0.341  Sum_probs=21.4

Q ss_pred             HHHHHHHHHH-------HHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           18 DVVRMMEQLR-------TEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        18 DAir~lkqLr-------~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      ||+.|||+-.       ++++.|+.+|+.|+.++..|+.+-.||+.+
T Consensus         2 ~AlefIk~~LG~~~p~~~d~eaLk~E~~eLk~k~~~L~~~~~el~~~   48 (53)
T 2yy0_A            2 SALDFLKHHLGAATPENPEIELLRLELAEMKEKYEAIVEENKKLKAK   48 (53)
T ss_dssp             --------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6778887764       477777777777777777777776666654

>3he5_B Synzip2; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=96.00  E-value=0.02  Score=36.74  Aligned_cols=42  Identities=29%  Similarity=0.398  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKE   66 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke   66 (136)
                      -||..+.+||+.|-.|+.+-+.|..-.-.||||..+|+.|..
T Consensus         7 ylrkkiarlkkdnlqlerdeqnlekiianlrdeiarleneva   48 (52)
T 3he5_B            7 YLRKKIARLKKDNLQLERDEQNLEKIIANLRDEIARLENEVA   48 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHHHHHHHHHh
Confidence            489999999999999999888888888888888887776654

>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1

Probab=95.96  E-value=0.015  Score=39.39  Aligned_cols=39  Identities=21%  Similarity=0.345  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +|++|..++..|+..+..              |..|+..|+.+++.|..+++.
T Consensus        30 ~i~~LE~~v~~le~~~~~--------------l~~en~~Lr~~i~~L~~El~~   68 (70)
T 1gd2_E           30 HLKALETQVVTLKELHSS--------------TTLENDQLRQKVRQLEEELRI   68 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHH--------------HHHHHHHHTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHH
Confidence            455555555555554444              445555555555555555443

>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=95.86  E-value=0.025  Score=36.91  Aligned_cols=36  Identities=39%  Similarity=0.496  Sum_probs=15.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           37 TEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        37 n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +..|+.+...|+.+..+|+.+...|+.|+..|...|
T Consensus        25 ~~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk~~l   60 (63)
T 2wt7_A           25 TDTLQAETDQLEDEKSALQTEIANLLKEKEKLEFIL   60 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444444433

>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus norvegicus}

Probab=95.61  E-value=0.071  Score=37.58  Aligned_cols=48  Identities=23%  Similarity=0.497  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      ..|..+++.|+.+-+.|..++..|..|+.+|..|...++.+.++|..+
T Consensus         7 ~~l~~eL~~l~~eE~~L~~eL~~lEke~~~l~~el~~le~E~~~L~~e   54 (96)
T 3q8t_A            7 EQLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQE   54 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhH
Confidence            667888888888888888888888888888888888888888888764

>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=95.58  E-value=0.056  Score=34.78  Aligned_cols=39  Identities=23%  Similarity=0.359  Sum_probs=24.2

Q ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           34 KQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        34 k~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      |..+..|+.+...|+.+..+|+.+...|+.|+..|.++|
T Consensus        21 k~~~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~Lk~~l   59 (61)
T 1t2k_D           21 KVWVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLKQLL   59 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345566666666666666666666666666666665554

>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=95.47  E-value=0.0036  Score=41.19  Aligned_cols=23  Identities=22%  Similarity=0.368  Sum_probs=20.7

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEA   30 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~   30 (136)
                      .|..||+||..||.||++|+.|+
T Consensus        39 ~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A           39 AAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             CcccHHHHHHHHHHHHHHHHHHh
Confidence            68889999999999999998764

>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=95.23  E-value=0.058  Score=34.69  Aligned_cols=33  Identities=24%  Similarity=0.383  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNEL   54 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnEL   54 (136)
                      ++.+|..++..|..+|..|.+++..|..|...|
T Consensus        23 ~~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~L   55 (61)
T 1t2k_D           23 WVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQL   55 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555555544444444444433

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=95.20  E-value=0.21  Score=36.18  Aligned_cols=60  Identities=27%  Similarity=0.446  Sum_probs=44.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH-----------HHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKA-----------EKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~-----------EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      =|++.-|-|..|+.|++.|+..+.+|+..+.++..           ..++|..+...++.+.++.-++++.
T Consensus        37 Ei~elrr~iq~L~~el~~l~~~~~~LE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~~r~e~~~ql~EYq~  107 (129)
T 3tnu_B           37 EISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQRGELALKDARNKLAELEEALQKAKQDMARLLREYQE  107 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            36777788889999999999999999887766543           3456666777777777776666665

>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D

Probab=94.91  E-value=0.13  Score=33.38  Aligned_cols=34  Identities=29%  Similarity=0.501  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR   55 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELr   55 (136)
                      .+.+|..++..|+.+|..|..++..|..|+..|+
T Consensus        24 ~~~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk   57 (63)
T 2wt7_A           24 LTDTLQAETDQLEDEKSALQTEIANLLKEKEKLE   57 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3555556666666666666655555555555444

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=94.83  E-value=0.14  Score=37.76  Aligned_cols=68  Identities=21%  Similarity=0.362  Sum_probs=42.1

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHHHHHHhh----HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQKLKQST----EDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n----~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .+.+|-.+|-.=-+-|.+|+.++++++.+.    ..|...+..|..|..+-|..++....|.+.|..++..+
T Consensus         9 ~~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            9 NKDEKDHLIERLYREISGLKAQLENMKTESQRVVLQLKGHVSELEADLAEQQHLRQQAADDCEFLRAELDEL   80 (120)
T ss_dssp             -CCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555555444555666666666666543    34455566777777777777777777777777777654

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=94.81  E-value=0.18  Score=36.87  Aligned_cols=52  Identities=31%  Similarity=0.427  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHH----HHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAE----KNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~E----KnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .++|+..+++|+-+++.+.++.+....|    -|.|++|.+.|+...+.|...++.
T Consensus         5 ~rdL~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iRe   60 (111)
T 2v66_B            5 NRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRE   60 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3567777777777777666665555443    444555555555555555544443

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=94.79  E-value=0.088  Score=44.82  Aligned_cols=53  Identities=21%  Similarity=0.348  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +.+|+.|++.|+++...|+++++.++.|..+|.++-...+...-+|.++++.+
T Consensus         5 ~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~rr~l~n~~~el   57 (403)
T 4etp_A            5 IAALKEKIAALKEKIAALKEKIKDTELGMKELNEILIKEETVRRTLHNELQEL   57 (403)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            45788999999999999999999999999999998888888888898888885

>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=94.75  E-value=0.057  Score=39.03  Aligned_cols=42  Identities=26%  Similarity=0.411  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCCCCCCC
Q 032660           42 EKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSGFLP   83 (136)
Q Consensus        42 ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~~p~f~p   83 (136)
                      ++...|+.|..+|+.|+.+|+.+|+.||-+|......-.|-|
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            345555566666666666666666666666666554444544

>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=94.75  E-value=0.045  Score=35.38  Aligned_cols=37  Identities=32%  Similarity=0.497  Sum_probs=17.1

Q ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           35 QSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        35 ~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      +.+..|+.++..|+.|.++|+.+...|+.|+..|.++
T Consensus        22 ~~~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~~Lk~~   58 (62)
T 1jnm_A           22 ERIARLEEKVKTLKAQNSELASTANMLREQVAQLKQK   58 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444455555555555555555444444444444443

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=94.74  E-value=0.32  Score=37.48  Aligned_cols=53  Identities=17%  Similarity=0.185  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .|.+|+++...|+..+..|.+++++-..--..|+||...|..+..-+|..++.
T Consensus        69 ~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE~kl~k  121 (152)
T 3a7p_A           69 TLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKLSD  121 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444444444444444444433333446777777777776666666554

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1

Probab=94.70  E-value=0.16  Score=33.14  Aligned_cols=32  Identities=25%  Similarity=0.403  Sum_probs=12.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           37 TEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        37 n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      ...|+.+.++|+.+-.+|+.+...|+.|+.-|
T Consensus        25 ~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~L   56 (63)
T 1ci6_A           25 QEALTGECKELEKKNEALKERADSLAKEIQYL   56 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333333333

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=94.60  E-value=0.25  Score=35.92  Aligned_cols=59  Identities=22%  Similarity=0.344  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH-----------HHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKA-----------EKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~-----------EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |++.-|-|..|+.|++.|+..+.+|+..+.++..           ..++|..+...++.+.++.-.+++.
T Consensus        40 i~elrr~iq~L~~el~~l~~~~~sLE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~~r~em~~ql~EYq~  109 (131)
T 3tnu_A           40 ISELRRTMQNLEIELQSQLSMKASLENSLEETKGRYCMQLAQIQEMIGSVEEQLAQLRCEMEQQNQEYKI  109 (131)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5667778888999999999999999887765543           3445666666777776666666655

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=94.43  E-value=0.28  Score=38.26  Aligned_cols=55  Identities=20%  Similarity=0.421  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHh
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE----QQVKA   74 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le----~qlk~   74 (136)
                      -..+++|.+.++.|..+.+.+.+....+..|+..|.|..+.|+.++.+++    -+||+
T Consensus        89 se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r~L~Ekl~~lEKe~a~~eid~~~eLKa  147 (168)
T 3o0z_A           89 SEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEAQDMLNHSEKEKNNLEIDLNYKLKS  147 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            34566777777777777777777777777777777777777777777776    44554

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=94.43  E-value=0.044  Score=45.16  Aligned_cols=27  Identities=15%  Similarity=0.299  Sum_probs=17.6

Q ss_pred             HHHHHHHhHHHHHHHHHHHHhccCCCC
Q 032660           54 LRDEKQRLKADKEKLEQQVKAMSAPSG   80 (136)
Q Consensus        54 LrdEk~~Lk~eke~Le~qlk~~~~~p~   80 (136)
                      |.++...++.|+++|+.|++.+..||.
T Consensus        73 L~~~Lk~ar~El~~LkeElerL~sPPL   99 (251)
T 3m9b_A           73 LMETLKEARQQLLALREEVDRLGQPPS   99 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSCCE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            556666666666666666777667764

>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=94.26  E-value=0.54  Score=34.09  Aligned_cols=60  Identities=17%  Similarity=0.351  Sum_probs=31.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           15 ILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        15 IL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+.|+-..+..|..+-..|......|++...+.....++|..+|..|..+++.|+.++..
T Consensus        63 ~l~e~EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~Lk~~led  122 (129)
T 2fxo_A           63 NLADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSELKRDIDD  122 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355666666666555555555555555555554444445555555555555555544443

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=94.25  E-value=0.24  Score=35.61  Aligned_cols=54  Identities=19%  Similarity=0.427  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      +.+||.++.+|+.++.....++..|..+-.+-+.......+++.+++++|..++
T Consensus         7 ~e~lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLT   60 (97)
T 2eqb_B            7 YNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLT   60 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666666666666666666666666666666666666677777787777653

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1

Probab=94.22  E-value=0.37  Score=31.38  Aligned_cols=46  Identities=28%  Similarity=0.349  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKAD   64 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~e   64 (136)
                      |.|+=..=+.+++.|..+...|+.++.+|+.+.+.|+.|...|+.-
T Consensus        14 A~R~R~KKk~~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~Lk~l   59 (63)
T 1ci6_A           14 ATRYRQKKRAEQEALTGECKELEKKNEALKERADSLAKEIQYLKDL   59 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344333344455555555555555555555555555555555543

>2oqq_A Transcription factor HY5; homodimer leucine zipper; 2.00A {Arabidopsis thaliana}

Probab=94.14  E-value=0.18  Score=31.51  Aligned_cols=36  Identities=22%  Similarity=0.491  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRD   56 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrd   56 (136)
                      .||.+|-.++..|...|..|++.+..|..|-.=||.
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            489999999999999999999999999877666663

>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=94.13  E-value=0.16  Score=34.86  Aligned_cols=48  Identities=19%  Similarity=0.205  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      -|.+|+..+++--+++...++.|++|..+..|..++.+.|+++.++++
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            388888888888888888889999999999999999998888888764

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=94.05  E-value=0.24  Score=47.15  Aligned_cols=16  Identities=38%  Similarity=0.690  Sum_probs=6.3

Q ss_pred             HHHHHHHhHHHHHHHH
Q 032660           54 LRDEKQRLKADKEKLE   69 (136)
Q Consensus        54 LrdEk~~Lk~eke~Le   69 (136)
                      |++||+.|+.+++.|+
T Consensus      1028 L~~e~~~L~qq~~~l~ 1043 (1080)
T 2dfs_A         1028 LKEQNTLLKTEKEELN 1043 (1080)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3333444444444443

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=94.03  E-value=0.45  Score=37.59  Aligned_cols=52  Identities=31%  Similarity=0.416  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHH----HHHHHHHHHHhHHHHHHHHHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAE----KNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~E----KnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      -.++|++++++|+.++..+..+.+....|    -|.|++|.+.|+..++.|...+.
T Consensus        57 ~~~~L~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~el~~l~~~~~~l~~~ir  112 (189)
T 2v71_A           57 RNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVR  112 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35566666666666666665555555444    55555555555555555555443

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A

Probab=93.98  E-value=0.068  Score=34.53  Aligned_cols=30  Identities=23%  Similarity=0.385  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           44 IKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        44 ~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +.+|..+-.+|..++..|+.++..|+.++.
T Consensus        24 ~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~   53 (62)
T 1jnm_A           24 IARLEEKVKTLKAQNSELASTANMLREQVA   53 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444433

>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=93.96  E-value=0.41  Score=32.97  Aligned_cols=37  Identities=30%  Similarity=0.454  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHHHHH-------HHHHHHhHHHHHHHHHHHHhc
Q 032660           39 DLQEKIKELKAEKNEL-------RDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        39 ~L~ee~~~L~~EKnEL-------rdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .|++....|..|||.|       .+...+|.+.+-.|+.+++-+
T Consensus        39 ele~~~~~l~~ek~~L~~ql~eaEe~~~~L~~~K~eLE~~l~el   82 (89)
T 3bas_A           39 ELEEQNVTLLEQKNDLFGSMKQLEDKVEELLSKNYHLENEVARL   82 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444455555554       444445566666666666654

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=93.88  E-value=0.079  Score=43.66  Aligned_cols=41  Identities=20%  Similarity=0.326  Sum_probs=36.4

Q ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           30 AQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        30 ~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      +..|+.++..|.+.+++|+.+.+++|+|...||.|+++|.+
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            55788888899999999999999999999999999998864

>3cve_A Homer protein homolog 1; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, postsynaptic cell membrane, synapse; 1.75A {Rattus norvegicus}

Probab=93.87  E-value=0.3  Score=33.40  Aligned_cols=50  Identities=12%  Similarity=0.290  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+..+++.++.+|..|++.++.|+...++-+.+-.+++.|..++..+|-.
T Consensus         4 ~~~~kLq~~E~~N~~Le~~v~~le~~Le~s~~~q~~~~~Elk~~~e~Ld~   53 (72)
T 3cve_A            4 NSHMKLQEVEIRNKDLEGQLSEMEQRLEKSQSEQDAFRSNLKTLLEILDG   53 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            46678899999999999999999999999999989999998888877643

>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=93.77  E-value=0.25  Score=41.85  Aligned_cols=11  Identities=27%  Similarity=0.299  Sum_probs=4.0

Q ss_pred             HHHHHHHHHHh
Q 032660           64 DKEKLEQQVKA   74 (136)
Q Consensus        64 eke~Le~qlk~   74 (136)
                      |..++.++++.
T Consensus       566 e~~~~~~~~~~  576 (597)
T 3oja_B          566 ETSLKRQKVKQ  576 (597)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            33333333333

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=93.67  E-value=0.72  Score=32.31  Aligned_cols=57  Identities=21%  Similarity=0.379  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +-|+=|++||-.+..|..+...-+-+.+.-|.|...|++....=.+|+++|+.|+-+
T Consensus        23 ~L~qEi~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l~~   79 (81)
T 3qh9_A           23 ELLQELRHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQLSR   79 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHHhh
Confidence            456778888888888877776666777888888888888888888899999988754

>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=93.65  E-value=0.23  Score=42.56  Aligned_cols=52  Identities=23%  Similarity=0.306  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ..|+.|+.+|++..+.|+++++.++.|..++.++......+.-+|.++++.+
T Consensus         6 ~~l~~el~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~rr~l~n~~~~l   57 (412)
T 3u06_A            6 AALSTEVVHLRQRTEELLRCNEQQAAELETCKEQLFQSNMERKELHNTVMDL   57 (412)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999999998888888888899998886

>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=93.44  E-value=0.23  Score=35.84  Aligned_cols=39  Identities=28%  Similarity=0.491  Sum_probs=33.2

Q ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           35 QSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        35 ~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ++..+|..+|.+|..|.+.||++|..|+.++++..  +++=
T Consensus        12 e~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~~--l~Gd   50 (100)
T 1go4_E           12 EEADTLRLKVEELEGERSRLEEEKRMLEAQLERRA--LQGD   50 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS--CCSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--hccc
Confidence            46778888999999999999999999999999864  6553

>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=93.43  E-value=0.29  Score=33.01  Aligned_cols=34  Identities=18%  Similarity=0.419  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           42 EKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        42 ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ..+++|..+-.+|++++..|..|.+.|..++..|
T Consensus        29 ~~i~~LE~~v~~le~~~~~l~~en~~Lr~~i~~L   62 (70)
T 1gd2_E           29 DHLKALETQVVTLKELHSSTTLENDQLRQKVRQL   62 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555666666666666666666665543

>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=93.42  E-value=0.39  Score=30.76  Aligned_cols=37  Identities=19%  Similarity=0.340  Sum_probs=22.5

Q ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           32 KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      .|+..+..|......|..-..+-|++...|+.++++|
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            3444444555555555555666667777777777776

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=93.41  E-value=0.87  Score=31.74  Aligned_cols=34  Identities=21%  Similarity=0.603  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           41 QEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        41 ~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.+|.+|.....++.-||.+|..|+++|+.++..
T Consensus        55 e~~i~~Lr~~i~~~~~ek~~l~~e~dnl~~~~~~   88 (93)
T 3s4r_A           55 EEEMRELRRQVDQLTNDKARVEVERDNLAEDIMR   88 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666667777777777777777777766554

>1deb_A APC protein, adenomatous polyposis coli protein; coiled coil, tumor suppressor, structural protein; 2.40A {Homo sapiens} SCOP: h.1.18.1

Probab=93.37  E-value=0.56  Score=30.61  Aligned_cols=45  Identities=20%  Similarity=0.353  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      .||-.|++.||.+|..|+.|.++=....+.|.-|-..+|.=.-.|
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            588899999999999999888777766666666666655444333

>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=93.36  E-value=0.54  Score=37.26  Aligned_cols=19  Identities=16%  Similarity=0.323  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHhhHHHHHH
Q 032660           25 QLRTEAQKLKQSTEDLQEK   43 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee   43 (136)
                      .|+.++..|.++|..|+.+
T Consensus       136 ~~~~~~~~L~~e~~~l~~~  154 (213)
T 1ik9_A          136 ENQAKNEHLQKENERLLRD  154 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=93.27  E-value=0.65  Score=35.77  Aligned_cols=51  Identities=16%  Similarity=0.138  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ++++..+..|+.++..|+.+++.|+.|..|-..-...|+.|..-|+-|+..
T Consensus        64 ~~~~~~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~  114 (152)
T 3a7p_A           64 DALLNTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNV  114 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555555555555555555555555555555555555555555555443

>3vmx_A Voltage-gated hydrogen channel 1; coiled-coil, ION channel, ION transport, membrane protein; 1.45A {Mus musculus}

Probab=93.20  E-value=0.25  Score=31.61  Aligned_cols=40  Identities=28%  Similarity=0.341  Sum_probs=30.2

Q ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           28 TEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        28 ~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .++.+||+.|..|-..+.+|..-++++.       .||+||+.-|+.
T Consensus         4 q~l~kLKe~n~~L~~kv~~Le~~c~~~e-------QEieRL~~LLkq   43 (48)
T 3vmx_A            4 RQILRLKQINIQLATKIQHLEFSCSEKE-------QEIERLNKLLKQ   43 (48)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHccHHH-------HHHHHHHHHHHH
Confidence            4678999999999988888877776665       556666665554

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.15  E-value=0.12  Score=44.47  Aligned_cols=49  Identities=16%  Similarity=0.319  Sum_probs=38.8

Q ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCCCC
Q 032660           32 KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPSG   80 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~~p~   80 (136)
                      +|......|+.+++.|..|++.+++|...|+.|..+++.|++.+..+|.
T Consensus        46 dl~~~lk~le~~~~~L~~e~e~l~~~~~~~~~e~~~~~ee~~~l~~~~~   94 (428)
T 4b4t_K           46 DIYFKLKKLEKEYELLTLQEDYIKDEQRHLKRELKRAQEEVKRIQSVPL   94 (428)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSCE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence            4555556777788888888889999999999999999999999877664

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=93.09  E-value=0.53  Score=39.25  Aligned_cols=49  Identities=10%  Similarity=0.075  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +++..|.++.+...+..+++++.|+.|++.|+.+...+..++++-.+.|
T Consensus       424 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  472 (487)
T 3oja_A          424 VEQQSVQNNAIRDWDMYQHKETQLAEENARLKKLNGEADLALASANATL  472 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcchhhhhhhhhHHHHHHHHhhhhhhhhhhhhhhhHhcccHH
Confidence            3333333333333334444444444444444444333333333333333

>3cvf_A Homer-3, homer protein homolog 3; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, phosphoprotein, polymorphism; 2.90A {Homo sapiens}

Probab=93.07  E-value=0.35  Score=33.54  Aligned_cols=49  Identities=18%  Similarity=0.389  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +..+++.++.+|..|++.++.|....++-+.+-.+++.|..++.++|-.
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            4567888999999999999999999999998888999998888877643

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A*

Probab=93.04  E-value=0.081  Score=35.95  Aligned_cols=24  Identities=21%  Similarity=0.315  Sum_probs=21.7

Q ss_pred             chhhhHHHHHHHHHHHHHHHHHHH
Q 032660           11 DKATILSDVVRMMEQLRTEAQKLK   34 (136)
Q Consensus        11 DKAsIL~DAir~lkqLr~e~~~Lk   34 (136)
                      .|.+||..||.|++.|+.+++++.
T Consensus        42 sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A           42 TKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHh
Confidence            688999999999999999988764

>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=92.99  E-value=0.52  Score=34.89  Aligned_cols=21  Identities=33%  Similarity=0.387  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHHhhHHHHHHHH
Q 032660           25 QLRTEAQKLKQSTEDLQEKIK   45 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~   45 (136)
                      .|+.+...|+.++..|..++.
T Consensus        26 ~l~~eN~~Lk~e~e~l~~~~~   46 (155)
T 2oto_A           26 RLRHENKDLKARLENAMEVAG   46 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            555555555555555544333

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=92.98  E-value=0.9  Score=35.40  Aligned_cols=60  Identities=17%  Similarity=0.357  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |.|+=..++.-..-+++||+.+..+.-....+....+||++-...|...+..|++++-.+
T Consensus        15 L~E~n~kLk~EsE~~~rlkK~~tEl~k~~~~~E~~~rELq~~~~~L~~~k~~Leke~~~L   74 (168)
T 3o0z_A           15 LEEANDLLRTESDTAVRLRKSHTEMSKSISQLESLNRELQERNRILENSKSQTDKDYYQL   74 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346666666666777788888888888888888888888888888888888888776553

>3he5_A Synzip1; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=92.98  E-value=0.48  Score=30.02  Aligned_cols=24  Identities=29%  Similarity=0.462  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHH
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKI   44 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~   44 (136)
                      .+|.||..|+..|..+|++|..+.
T Consensus         3 nlvaqlenevaslenenetlkkkn   26 (49)
T 3he5_A            3 NLVAQLENEVASLENENETLKKKN   26 (49)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhhcccHHHHHhc
Confidence            367899999999999998887653

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=92.89  E-value=0.35  Score=33.89  Aligned_cols=38  Identities=21%  Similarity=0.338  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           38 EDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      +.=.....++..+-.+|..||..|+.+++.|+.++..+
T Consensus        32 ~krk~r~~e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~L   69 (87)
T 1hjb_A           32 DKAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTL   69 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444456666777778888888888888888877764

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=92.84  E-value=0.56  Score=37.03  Aligned_cols=28  Identities=21%  Similarity=0.328  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEK   51 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EK   51 (136)
                      ..|..|++.++.++..|++++.++..+.
T Consensus        93 ~aL~kEie~~~~~i~~lE~eile~~e~i  120 (256)
T 3na7_A           93 RSLNIEEDIAKERSNQANREIENLQNEI  120 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444433333

>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=92.83  E-value=0.46  Score=34.47  Aligned_cols=44  Identities=25%  Similarity=0.397  Sum_probs=28.8

Q ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           31 QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        31 ~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+|......|+..++++.....+..+.+..|.+++.+|++++..
T Consensus        72 ~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~  115 (129)
T 2fxo_A           72 DQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSE  115 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555666666667666667777777777777777766654

>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=92.68  E-value=1.1  Score=27.95  Aligned_cols=53  Identities=13%  Similarity=0.183  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      -+.+|...+..++.....+..+...++..-+.+.++......+|.+++.|+..
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            35566666666766666677777777777777777777777777777777654

>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=92.63  E-value=0.88  Score=38.48  Aligned_cols=44  Identities=23%  Similarity=0.380  Sum_probs=24.4

Q ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           31 QKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        31 ~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ++|+++.+.++..+++-+....||++|++.+++|+..|++.+..
T Consensus       540 ~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~~~~  583 (597)
T 3oja_B          540 EDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAKKNR  583 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             hhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            33334444455555555555566666666666666666665544

>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=92.56  E-value=0.23  Score=33.33  Aligned_cols=33  Identities=27%  Similarity=0.440  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           44 IKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        44 ~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      |+.|..+..+|+.|+..|+.+.+.|+++|.++.
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            455666666666777777777777777776653

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=92.54  E-value=0.11  Score=33.37  Aligned_cols=29  Identities=17%  Similarity=0.289  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           44 IKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        44 ~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +.+|..+...|..||..|+.+++.|++++
T Consensus        24 ~~~LE~~v~~L~~eN~~L~~~~~~L~~~~   52 (55)
T 1dh3_A           24 VKSLENRVAVLENQNKTLIEELKALKDLY   52 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44555555555566666666666655443

>1zhc_A Hypothetical protein HP1242; A-helical protein, unknown function; NMR {Helicobacter pylori}

Probab=92.34  E-value=0.23  Score=33.59  Aligned_cols=57  Identities=16%  Similarity=0.313  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH------HHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKA------EKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~------EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |.|.-|++=..+..+|.+++..|..+|+.+..      +..+|+-+|..||-+|.++-.+.+.
T Consensus         7 d~I~~Lk~~d~~f~~L~~eH~~LD~~I~~le~~~~~~~~l~~LKk~KL~LKDeI~~lL~~~~~   69 (76)
T 1zhc_A            7 DEISVLKANNPHFDKIFEKHNQLDDDIKTAEQQNASDAEVSHMKKQKLKLKDEIHSMIIEYRE   69 (76)
T ss_dssp             HHHHHSTTTSTTHHHHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            44444444444455555555555555554432      5677777888888777777665543

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=92.32  E-value=0.91  Score=35.81  Aligned_cols=45  Identities=13%  Similarity=0.151  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      |..++..|+.....++.++.+++.+...+..+...+++.+++.+.
T Consensus        37 le~~~~~l~~~~~~~~~~l~d~~~~~~~~e~~i~~~~~ri~~~~~   81 (256)
T 3na7_A           37 ALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQK   81 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333333333333333333333333

>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=92.30  E-value=0.56  Score=30.03  Aligned_cols=39  Identities=31%  Similarity=0.451  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL   61 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~L   61 (136)
                      +.+|+.++..|.+.|+.|.+..+.-..|...|++|..+|
T Consensus        11 ~~~l~~~l~~L~~rN~rL~~~L~~AR~el~~Lkeele~L   49 (51)
T 3m91_A           11 IHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999999887765

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=92.18  E-value=2.2  Score=31.26  Aligned_cols=48  Identities=19%  Similarity=0.246  Sum_probs=34.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 032660           14 TILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL   61 (136)
Q Consensus        14 sIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~L   61 (136)
                      .|..++=++|.+|++++..|+.+.+.=.........|.+.||.|+..|
T Consensus        33 ~l~~E~q~~v~ql~~~i~~Le~eL~e~r~~~q~a~~e~e~Lr~e~~~l   80 (120)
T 3i00_A           33 NMKTESQRVVLQLKGHVSELEADLAEQQHLRQQAADDCEFLRAELDEL   80 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            577888899999999999988887776655555555555555555544

>2wt7_B Transcription factor MAFB; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 2wty_A* 1k1v_A

Probab=91.94  E-value=0.49  Score=33.50  Aligned_cols=41  Identities=17%  Similarity=0.363  Sum_probs=30.6

Q ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           35 QSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        35 ~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .+...|+.+...|..|...|+.|+..+..|++.+.+.++.+
T Consensus        48 ~q~~~LE~e~~~L~~e~~~L~~e~~~~~~e~d~~k~k~~~L   88 (90)
T 2wt7_B           48 QQKHHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKSEKL   88 (90)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34566777777777777788888888888888777777765

>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=91.81  E-value=0.27  Score=29.53  Aligned_cols=26  Identities=35%  Similarity=0.492  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           38 EDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      ..|+++..+|-.|+++|++|..+||+
T Consensus         4 nQLE~kVEeLl~~n~~Le~eV~rLk~   29 (34)
T 2oxj_A            4 XQLEXKVXELLXKNXHLEXEVXRLKX   29 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence            45777777777777777777777764

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=91.69  E-value=0.78  Score=43.65  Aligned_cols=21  Identities=14%  Similarity=0.213  Sum_probs=11.8

Q ss_pred             HHHHHHhHHHHHHHHHHHHhc
Q 032660           55 RDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        55 rdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ++..+.|+.|+.+|++|+..+
T Consensus      1022 ~~kv~~L~~e~~~L~qq~~~l 1042 (1080)
T 2dfs_A         1022 EQLVSELKEQNTLLKTEKEEL 1042 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333445666666666666554

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=91.58  E-value=1.4  Score=34.76  Aligned_cols=54  Identities=24%  Similarity=0.308  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHH----HHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEK----IKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee----~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      .|.-.-+.+|+.|++.+|..+.....+    +..|..|...||+++..|+..+-.||+
T Consensus        59 ~~L~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~el~~l~~~~~~l~~~ireLEq  116 (189)
T 2v71_A           59 RDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQ  116 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455566666666666666655555    566666666666666666666655554

>3oa7_A Head morphogenesis protein, chaotic nuclear migra protein 67 fusion protein; coiled coils, structural protein, spindle POLE BODY; 2.30A {Bacillus phage PHI29}

Probab=91.53  E-value=0.7  Score=37.22  Aligned_cols=45  Identities=24%  Similarity=0.316  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL   61 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~L   61 (136)
                      ++-++.|.|||++.-.--.+...|+.++.+|.+|+|+||..-..|
T Consensus        26 ~~~~~~~~~~~a~~~s~~s~~~dl~~s~~~l~ae~~~L~~~l~kL   70 (206)
T 3oa7_A           26 SERTEALQQLRVNYGSFVSEYNDLTKSHNTLSKELDNLRSRFGNL   70 (206)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHc
Confidence            455666777766655555555555555555554444444444333

>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=91.46  E-value=0.38  Score=30.74  Aligned_cols=29  Identities=21%  Similarity=0.442  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           44 IKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        44 ~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      ...|+.|..|||.+...|+.+.+.|..+|
T Consensus        21 ~eaLk~E~~eLk~k~~~L~~~~~el~~~l   49 (53)
T 2yy0_A           21 IELLRLELAEMKEKYEAIVEENKKLKAKL   49 (53)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=91.33  E-value=0.41  Score=33.51  Aligned_cols=43  Identities=28%  Similarity=0.357  Sum_probs=32.0

Q ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           32 KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +=|.....++.+..+|+.|-..|+.+...|+.|...|.+.|..
T Consensus        33 krk~r~~e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~Lr~ll~~   75 (87)
T 1hjb_A           33 KAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTLRNLFKQ   75 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455566777778888888888888888888888877776654

>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=91.27  E-value=0.74  Score=31.56  Aligned_cols=41  Identities=22%  Similarity=0.328  Sum_probs=30.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcc
Q 032660           36 STEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMS   76 (136)
Q Consensus        36 ~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~   76 (136)
                      +-+.=.....++..+-.+|..||..|+.+++.|+.++..+.
T Consensus        30 SR~krk~r~~e~~~r~~~L~~eN~~L~~~v~~L~~E~~~Lr   70 (78)
T 1gu4_A           30 SRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTLR   70 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444445567777888888899999999999988887753

>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}

Probab=91.22  E-value=1.1  Score=39.53  Aligned_cols=52  Identities=19%  Similarity=0.357  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHH-----------HHHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEK-----------NELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EK-----------nELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      -++|+.+++.|+++...+..+|..++..+           .+|++|...|+.++..|+.+++.
T Consensus        79 ~r~~~~~~~~l~~~rn~~sk~i~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~  141 (501)
T 1wle_A           79 LRQLREQIRSLEEEKEAVTEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQ  141 (501)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTGGGCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45666777777777777776666555322           35555555555555555444333

>1gk6_A Vimentin; intermediate filament, dimer, parallel coiled coil, heptad repeat, leucine zipper, fusion protein; 1.9A {Saccharomyces cerevisiae} SCOP: h.1.20.1

Probab=91.20  E-value=0.58  Score=30.11  Aligned_cols=47  Identities=21%  Similarity=0.299  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      |++++..+..|+++...+..++.....|-.+|.+=|.+|..||.---
T Consensus         2 l~~~q~~i~~le~el~~~r~e~~~q~~eYq~LlniK~~Le~EIatYR   48 (59)
T 1gk6_A            2 MKQLEDKVEELLSKNYHLENEVARLKKLVGDLLNVKMALDIEIATYR   48 (59)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            35778888888888888888888888888999999999998886443

>3v86_A De novo design helix; computational design of A protein crystal, helical coil, DE designed helix, de novo protein; 2.91A {Synthetic}

Probab=91.16  E-value=0.21  Score=28.31  Aligned_cols=25  Identities=32%  Similarity=0.549  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKEL   47 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L   47 (136)
                      +-||..|+-+||-+...|.+|.++|
T Consensus         2 vyqlkdevgelkgevralkdevkdl   26 (27)
T 3v86_A            2 VYQLKDEVGELKGEVRALKDEVKDL   26 (27)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhhHHHHHHHhHHHHHHHHHhcc
Confidence            4567777777777766666666655

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=91.08  E-value=0.15  Score=41.28  Aligned_cols=26  Identities=27%  Similarity=0.571  Sum_probs=21.7

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHHHH
Q 032660            4 PGRPPKTDKATILSDVVRMMEQLRTE   29 (136)
Q Consensus         4 P~rp~K~DKAsIL~DAir~lkqLr~e   29 (136)
                      |+-..|+||++||..||.||+.|+..
T Consensus        39 p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           39 PGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             CSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            43346999999999999999998753

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=90.90  E-value=2.3  Score=30.98  Aligned_cols=54  Identities=24%  Similarity=0.308  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHH----HHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEK----IKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee----~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      |=-.-+.+|+.|++.+|..+...+.+    +..|..|...||+++..|+..+-.||+.
T Consensus         7 dL~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~   64 (111)
T 2v66_B            7 DLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQA   64 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33445667777777777777766654    5667777777777777777777777654

>2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: SSA; 2.60A {Pyrococcus horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A* 2zr3_A

Probab=90.80  E-value=2.2  Score=36.77  Aligned_cols=53  Identities=17%  Similarity=0.287  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHH----------HHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKE----------LKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~----------L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      -++|+.+++.|+++...+..+|..          |+.|..+|+++...|+.+...++.++..+
T Consensus        40 ~r~~~~~~~~l~~~~n~~sk~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (455)
T 2dq0_A           40 WRTKLKEINRLRHERNKIAVEIGKRRKKGEPVDELLAKSREIVKRIGELENEVEELKKKIDYY  102 (455)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            466777788888888888777764          45555555666666666666666666653

>3s9g_A Protein hexim1; cyclin T-binding domain (TBD), cyclin T1/P-TEFB/7SK snRNA, N transcription; 2.10A {Homo sapiens} PDB: 2gd7_A

Probab=90.78  E-value=1.6  Score=31.84  Aligned_cols=55  Identities=20%  Similarity=0.418  Sum_probs=32.7

Q ss_pred             CCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHH-------HHHHHHHHHHHHHHHHHHhHHHHHH
Q 032660            9 KTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQE-------KIKELKAEKNELRDEKQRLKADKEK   67 (136)
Q Consensus         9 K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~e-------e~~~L~~EKnELrdEk~~Lk~eke~   67 (136)
                      .|.|.-+|-|-+.    |-....+|.++|..|+.       .+++|..|...||.||+.|+.|-+-
T Consensus        29 ~mSKqELIqEYl~----LE~~~s~le~e~~rlr~~~~~~~~~v~eLe~everL~~ENq~L~~e~~~   90 (104)
T 3s9g_A           29 NMSKQELIKEYLE----LEKSLSRMEDENNRLRLESKRLDARVRELELELDRLRAENLQLLTENEL   90 (104)
T ss_dssp             TSCHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHHHHH----HHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3556555555543    44455556666665555       5666777777777777766665443

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=90.74  E-value=1.2  Score=36.98  Aligned_cols=33  Identities=15%  Similarity=0.245  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           42 EKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        42 ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .+.+....|-+.|++|+.+|+.+++++..++..
T Consensus       435 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  467 (487)
T 3oja_A          435 RDWDMYQHKETQLAEENARLKKLNGEADLALAS  467 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHhhhhhhhhhhhhhhhHh
Confidence            344444555566666777777777777666655

>2dgc_A Protein (GCN4); basic domain, leucine zipper, DNA binding, eukaryotic regulatory protein, transcription/DNA complex; HET: DNA; 2.20A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 1dgc_A* 1ld4_E 1ysa_C* 3p8m_D

Probab=90.69  E-value=0.35  Score=31.65  Aligned_cols=34  Identities=21%  Similarity=0.356  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           40 LQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        40 L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      =++.+.+|..+-.+|..||..|+++++.|.+++.
T Consensus        28 K~~~~~~Le~~v~~L~~eN~~L~~ev~~Lr~~l~   61 (63)
T 2dgc_A           28 KLQRMKQLEDKVEELLSKNYHLENEVARLKKLVG   61 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3445566666666667777777777777776654

>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus norvegicus}

Probab=90.68  E-value=1.3  Score=30.97  Aligned_cols=14  Identities=21%  Similarity=0.480  Sum_probs=5.1

Q ss_pred             HhHHHHHHHHHHHH
Q 032660           60 RLKADKEKLEQQVK   73 (136)
Q Consensus        60 ~Lk~eke~Le~qlk   73 (136)
                      .++.+.-.++.+++
T Consensus        64 ~~~~ql~e~~dE~~   77 (96)
T 3q8t_A           64 EFKRQQLELDDELK   77 (96)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333333333333

>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}

Probab=90.67  E-value=1.9  Score=37.85  Aligned_cols=57  Identities=19%  Similarity=0.297  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHH-----------HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQ-----------EKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~-----------ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ...-+.+|+++.+++.+++..+.           ++...|+.|..+|+++...|+.+...++.++..+
T Consensus        82 ~~~~~~~l~~~rn~~sk~i~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~~~~~l~~~  149 (501)
T 1wle_A           82 LREQIRSLEEEKEAVTEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQLEEQFYLR  149 (501)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTGGGCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556788888888888777654           3667899999999999999999999999999884

>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=90.60  E-value=1.1  Score=34.33  Aligned_cols=15  Identities=20%  Similarity=0.581  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHhcc
Q 032660           62 KADKEKLEQQVKAMS   76 (136)
Q Consensus        62 k~eke~Le~qlk~~~   76 (136)
                      .+++.+++++|..++
T Consensus        78 E~~~~~ie~ElEeLT   92 (154)
T 2ocy_A           78 EEEADKLNKEVEDLT   92 (154)
T ss_dssp             HTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            466677777777643

>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=90.45  E-value=0.57  Score=32.58  Aligned_cols=32  Identities=38%  Similarity=0.519  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           43 KIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        43 e~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ++.+|+.|+.-|+.|..+++.-+.|++..++.
T Consensus        38 rvdELt~E~e~l~~El~s~~~~~~r~~~ri~e   69 (77)
T 2w83_C           38 KVDELTCEKDVLQGELEAVKQAKLKLEEKNRE   69 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555555555555555555555555443

>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=90.41  E-value=2  Score=32.08  Aligned_cols=10  Identities=30%  Similarity=0.471  Sum_probs=3.6

Q ss_pred             HHHHHHHHHH
Q 032660           40 LQEKIKELKA   49 (136)
Q Consensus        40 L~ee~~~L~~   49 (136)
                      |+.||+.|+.
T Consensus        76 LqgEI~~Lnq   85 (121)
T 3mq7_A           76 LEGEITTLNH   85 (121)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            3333333333

>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=90.39  E-value=0.76  Score=38.64  Aligned_cols=56  Identities=16%  Similarity=0.136  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ++.=++.|+.|+.+|+..+....++++.|+....+++...+.|+..+..|+..+..
T Consensus         3 ~~~~~~~~~~~~~~~e~~i~~~~~~i~~L~~~l~~~~~~i~~l~~~i~~l~~~~~~   58 (323)
T 1lwu_C            3 GQKTVQKILEEVRILEQIGVSHDAQIQELSEMWRVNQQFVTRLQQQLVDIRQTCSR   58 (323)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            44556778888888888888888888888877777777777777777666665543

>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=90.32  E-value=2.8  Score=28.98  Aligned_cols=50  Identities=24%  Similarity=0.365  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +.+-++|++.|+.....|.+-...|+.=.++|..|...|...++.|....
T Consensus        20 ~~q~qaEl~sLrrT~~EL~~G~~KL~~mi~~l~~E~~~l~~ni~~lk~K~   69 (78)
T 3iv1_A           20 MDRAQAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKD   69 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555555554444444555555555555555554433

>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=90.22  E-value=1.4  Score=30.27  Aligned_cols=39  Identities=23%  Similarity=0.331  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRL   61 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~L   61 (136)
                      ++.+..++++|++..+......++|......|-.||..|
T Consensus        16 m~~~eeel~~lke~l~k~e~~rkele~~~~~l~~ek~~L   54 (89)
T 3bas_A           16 MKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDL   54 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444444444444444

>3qne_A Seryl-tRNA synthetase, cytoplasmic; amino acid biosynthesis, CTG-clade, codon ambiguity, pathoge II aminoacyl-tRNA synthetase family; 2.00A {Candida albicans} PDB: 3qo7_A* 3qo8_A* 3qo5_A

Probab=90.21  E-value=2.6  Score=37.18  Aligned_cols=51  Identities=22%  Similarity=0.407  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHH----------HHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKE----------LKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~----------L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ++|+.+++.|+++...+..+|..          |.+|..+|+++...|+.+...++.++..
T Consensus        43 r~~~~~~~~l~~~rn~~sk~i~~~k~~~~~~~~l~~~~~~l~~~i~~le~~~~~~~~~~~~  103 (485)
T 3qne_A           43 VKLRFDLDEHNKKLNSVQKEIGKRFKAKEDAKDLIAEKEKLSNEKKEIIEKEAEADKNLRS  103 (485)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56777778888877777777654          4455556666666666666666666655

>3c3g_A Alpha/beta peptide with the GCN4-PLI SIDE chain S AN (alpha-alpha-beta) backbone; helix bundle, foldamer, unknown function protein; HET: HMR B3Q B3D B3E B3L BIL B3K BAL GOL; 1.80A {Synthetic} PDB: 3heu_A* 3het_A* 3hev_A* 3hew_A* 3hey_A* 3hex_A* 3c3h_A*

Probab=90.17  E-value=0.51  Score=28.15  Aligned_cols=26  Identities=15%  Similarity=0.371  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           38 EDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      ..|+++..+|-.++++|++|-.+||+
T Consensus         3 nQLEdKvEeLl~~~~~Le~EV~RLk~   28 (33)
T 3c3g_A            3 KXIEXKLXEIXSKXYHXENXLARIKX   28 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            35666777777777777777777664

>3trt_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural protein; 2.30A {Homo sapiens} PDB: 3klt_A*

Probab=90.07  E-value=1.4  Score=28.86  Aligned_cols=25  Identities=28%  Similarity=0.460  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           44 IKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        44 ~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      .+..+.|.+|||-..++|..|++.|
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            4444555555555555555554443

>3a2a_A Voltage-gated hydrogen channel 1; voltage-gated proton channel, alternative splicing, coiled C transport, ionic channel, membrane, transmembrane; 2.00A {Homo sapiens}

Probab=90.04  E-value=0.85  Score=30.16  Aligned_cols=41  Identities=24%  Similarity=0.340  Sum_probs=31.5

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      -.++.+||+-|.+|-.++..|+..++|-.       .||+||..-|+.
T Consensus        10 e~q~~kLKq~n~~L~~kv~~Le~~c~e~e-------QEieRL~~LLkq   50 (58)
T 3a2a_A           10 ERQLLRLKQMNVQLAAKIQHLEFSCSEKE-------QEIERLNKLLRQ   50 (58)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHH
Confidence            34678999999999999998887776654       567777777765

>3u1c_A Tropomyosin alpha-1 chain; anti-parallel coiled coil, contractIle protein; 1.80A {Gallus gallus} PDB: 3u1a_A

Probab=89.81  E-value=3.4  Score=28.89  Aligned_cols=48  Identities=17%  Similarity=0.266  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      +..|+.+.....+..+.++.+.+.+..+...+.+|..+|..-+..|+.
T Consensus        11 m~~lk~e~e~a~drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~   58 (101)
T 3u1c_A           11 MQMLKLDKENALDRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTED   58 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            444555555555555555555444444444444444444433333333

>2w6a_A ARF GTPase-activating protein GIT1; PIX, zinc, signaling protein, CAT-1, cytoplasm, ANK repeat, coiled-coil, zinc-finger, metal-binding; 1.40A {Rattus norvegicus}

Probab=89.79  E-value=0.89  Score=30.50  Aligned_cols=36  Identities=22%  Similarity=0.469  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      .+.||.|=+-|..|.+|++-+..+.+.|+.|++.|+
T Consensus        26 eAkiQQLmkVN~~ls~Elr~mQ~~lq~LQsen~~Lr   61 (63)
T 2w6a_A           26 EAKVQQLMKVNSSLSDELRKLQREIHKLQAENLQLR   61 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHhhhHHHHHHHHHHHHHHhhhhhhc
Confidence            456778888888888888888888888888887775

>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=89.76  E-value=0.47  Score=31.04  Aligned_cols=25  Identities=24%  Similarity=0.429  Sum_probs=10.8

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKEL   47 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L   47 (136)
                      +.+|..++..|+.+|..|..++..|
T Consensus        32 ~~~Le~~v~~L~~eN~~L~~ev~~L   56 (63)
T 2dgc_A           32 MKQLEDKVEELLSKNYHLENEVARL   56 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444443333

>2j5u_A MREC protein; bacterial cell shape determining protein MREC, cell shape regulation; 2.5A {Listeria monocytogenes}

Probab=89.71  E-value=0.16  Score=40.75  Aligned_cols=18  Identities=22%  Similarity=0.361  Sum_probs=7.2

Q ss_pred             HHHhhHHHHHHHHHHHHH
Q 032660           33 LKQSTEDLQEKIKELKAE   50 (136)
Q Consensus        33 Lk~~n~~L~ee~~~L~~E   50 (136)
                      |+++|+.|++++..|+.+
T Consensus        24 l~~eN~~Lk~e~~~l~~~   41 (255)
T 2j5u_A           24 TYTENQHLKERLEELAQL   41 (255)
T ss_dssp             --CTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            444444444444444433

>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=89.55  E-value=0.55  Score=27.99  Aligned_cols=23  Identities=39%  Similarity=0.570  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhH
Q 032660           40 LQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        40 L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      |+++..+|-.|+.+|++|-.+|+
T Consensus         5 LE~kVEeLl~~n~~Le~EV~RLk   27 (33)
T 3m48_A            5 LEAKVEELLSKNWNLENEVARLK   27 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHH
Confidence            44444444444444444444443

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=89.48  E-value=3.8  Score=28.41  Aligned_cols=50  Identities=20%  Similarity=0.316  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +.-|+.+.....+....++.+.+.+..+...+.+|...|+.-+..|++++
T Consensus        11 m~~lk~e~e~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~el   60 (101)
T 3u59_A           11 MQMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEV   60 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            44455555555555555555555555555555555555555544444443

>2no2_A HIP-I, huntingtin-interacting protein 1; clathrin light chain binding, HIP1 coiled-coil domain, endocytosis, clathrin SELF-assembly, cell adhesion; 2.80A {Homo sapiens}

Probab=89.35  E-value=3.3  Score=29.55  Aligned_cols=41  Identities=22%  Similarity=0.344  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHH-hhHHHHHHHHHHHHHHHHHHH
Q 032660           16 LSDVVRMMEQLRTEAQKLKQ-STEDLQEKIKELKAEKNELRD   56 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~-~n~~L~ee~~~L~~EKnELrd   56 (136)
                      -.|+.++.++|..++++++. ..+++++.+..|..-++||..
T Consensus        24 ~~e~e~~k~eL~~~~~~~~~~~~~k~~eq~~~le~lk~eL~~   65 (107)
T 2no2_A           24 QVDLEREKKELEDSLERISDQGQRKTQEQLEVLESLKQELAT   65 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35778888888888888763 444455555544444444443

>1ses_A Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A {Thermus thermophilus} SCOP: a.2.7.1 d.104.1.1 PDB: 1ser_A* 1set_A* 1sry_A

Probab=89.35  E-value=3.7  Score=34.96  Aligned_cols=54  Identities=19%  Similarity=0.356  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHH--------HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEK--------IKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee--------~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      --++++.+++.|+++...+..+        ...|+.|..+|+++...|+.+...++.++..+
T Consensus        36 ~~r~~~~~~~~l~~~~n~~sk~i~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (421)
T 1ses_A           36 EVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEAL   97 (421)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456666777777766666644        34667777777777777777777777777763

>1wt6_A Myotonin-protein kinase; coiled-coil, kinase activation, DMPK, molecular replacement, transferase; 1.60A {Homo sapiens}

Probab=89.33  E-value=2.8  Score=29.26  Aligned_cols=42  Identities=17%  Similarity=0.386  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEK   67 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~   67 (136)
                      ++.|+.+.|..|-.++.+.++......||..|...|+.+++.
T Consensus        29 i~EELs~vr~~ni~~eskL~eae~rn~eL~~e~~~l~~~~ee   70 (81)
T 1wt6_A           29 LSREMEAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMEL   70 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555556666666655555554444444444444444443

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1

Probab=89.28  E-value=1.8  Score=29.29  Aligned_cols=36  Identities=22%  Similarity=0.444  Sum_probs=17.4

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKEL   47 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L   47 (136)
                      +.++|+|=+    .+|+.=..=|+.|+.++..|+++...|
T Consensus        31 ~~~~k~sk~----~iL~kA~~yI~~L~~~~~~l~~e~~~L   66 (80)
T 1nlw_A           31 PDSSRHTTL----SLLTKAKLHIKKLEDSDRKAVHQIDQL   66 (80)
T ss_dssp             SSSCCCTTH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355665533    455555555555554444444433333

>1uix_A RHO-associated kinase; coiled-coil, transferase; HET: MSE; 1.80A {Bos taurus} SCOP: h.1.27.1

Probab=89.23  E-value=2.8  Score=28.54  Aligned_cols=49  Identities=27%  Similarity=0.403  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |...++-|..+++.|.+.++....|...+++|-....+.+.+++.+|+.
T Consensus         2 ~~k~v~~l~~E~eel~~klk~~~ee~~~~~eee~~~~~~k~~lek~L~~   50 (71)
T 1uix_A            2 STSDVANLANEKEELNNKLKEAQEQLSRLKDEEISAAAIKAQFEKQLLT   50 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455566666666666666666666666666666666666677766654

>1l8d_A DNA double-strand break repair RAD50 ATPase; zinc finger, DNA repair, recombination, HOOK motif, replication; HET: DNA CIT; 2.20A {Pyrococcus furiosus} SCOP: h.4.12.1

Probab=89.15  E-value=0.97  Score=31.11  Aligned_cols=44  Identities=20%  Similarity=0.358  Sum_probs=32.9

Q ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCC
Q 032660           35 QSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAP   78 (136)
Q Consensus        35 ~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~~   78 (136)
                      .+...+.+++.++..+.++|+++...++++++.++..+..+..+
T Consensus         3 ~~~~~~~~~~~~~~~~l~~L~~~~~~l~~~i~~l~~~l~~l~~~   46 (112)
T 1l8d_A            3 KLLEELETKKTTIEEERNEITQRIGELKNKIGDLKTAIEELKKA   46 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            44555666677777777888888888888888888888887653

>3c3f_A Alpha/beta peptide with the GCN4-PLI SIDE chain S AN (alpha-alpha-alpha-beta) backbone...; helix bundle, foldamer, unknown function, de novo protein; HET: B3K B3D B3E BIL B3L BAL; 2.00A {Synthetic} SCOP: h.1.3.1

Probab=89.08  E-value=0.65  Score=27.83  Aligned_cols=26  Identities=12%  Similarity=0.317  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           38 EDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      ..|+++..+|-.++++|++|-.+||.
T Consensus         4 nQLEdKVEeLl~~~~~Le~EV~RLk~   29 (34)
T 3c3f_A            4 XQIEXKLEXILSXLYHXENEXARIXK   29 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            45667777777777777777777764

>1x8y_A Lamin A/C; structural protein, intermediate filament protein; 2.20A {Homo sapiens} SCOP: h.1.20.1 PDB: 3v5b_A 3v4w_A 3v4q_A

Probab=89.06  E-value=1.9  Score=29.39  Aligned_cols=45  Identities=16%  Similarity=0.202  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEK   67 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~   67 (136)
                      +.+++..+..|+.+...+..++.....|-.+|.+=|.+|..||.-
T Consensus        30 l~~~q~~i~~lE~el~~~r~e~~~ql~EYq~LlnvK~~Le~EIat   74 (86)
T 1x8y_A           30 RDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHA   74 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            556666666666666666666666666777777777777777643

>3htk_A Structural maintenance of chromosomes protein 5; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=89.02  E-value=2.8  Score=26.07  Aligned_cols=48  Identities=25%  Similarity=0.273  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEK   67 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~   67 (136)
                      -+.+.++-.++..++.+...+..++..+..+.|..|++...++.+++.
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi~~   58 (60)
T 3htk_A           11 ENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEY   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345566666777777777888888888888888888888888877764

>1gk4_A Vimentin; intermediate filament, dimer, parallel coiled coil, heptad repeat, stutter; 2.3A {Homo sapiens} SCOP: h.1.20.1

Probab=89.01  E-value=1.8  Score=29.26  Aligned_cols=42  Identities=14%  Similarity=0.262  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADK   65 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~ek   65 (136)
                      ++++..+..|+.+...+..++...-.|-.+|.+=|.+|..||
T Consensus        29 ~~~q~~i~~lE~eL~~~r~e~~~q~~EYq~LlnvK~~Ld~EI   70 (84)
T 1gk4_A           29 ANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEI   70 (84)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH
Confidence            334444444444444444444444444444444444444444

>2wq1_A General control protein GCN4; TAA, nucleus, coiled coil, DNA-binding, protein export, ION coordination, polar core residues; 1.08A {Saccharomyces cerevisiae} PDB: 2wq0_A 2wq2_A 2wq3_A 2wpz_A 2wpy_A 1ij0_A 1ij1_A 1gcm_A 1rb5_A 1rb6_A 1rb1_A 1rb4_A 1swi_A 3k7z_A 1zii_A 1zij_A 1ij2_A 1ij3_A 1zil_A 1zim_A ...

Probab=88.85  E-value=0.73  Score=27.46  Aligned_cols=25  Identities=24%  Similarity=0.259  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           39 DLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        39 ~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      .|++++.+|..++++|.+|-.+|+.
T Consensus         4 QLEdKVEell~~~~~le~EV~Rl~~   28 (33)
T 2wq1_A            4 QLEDKIEENTSKIYHNTNEIARNTK   28 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            5667777777777777777666653

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=88.76  E-value=0.24  Score=40.79  Aligned_cols=21  Identities=43%  Similarity=0.491  Sum_probs=19.5

Q ss_pred             CCCchhhhHHHHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRT   28 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~   28 (136)
                      .|.||+|||-.||.|||.|+.
T Consensus        47 ~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B           47 RKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHC
T ss_pred             cccCHHHHHHHHHHHHHHhhc
Confidence            699999999999999999874

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=88.43  E-value=4.9  Score=29.45  Aligned_cols=27  Identities=19%  Similarity=0.182  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHH
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQE   42 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~e   42 (136)
                      |.-|=+.|..-..++.+||.+.+.+.+
T Consensus        33 L~~AEeaL~~Kq~~idelk~ei~q~~~   59 (110)
T 2v4h_A           33 LQQAEEALVAKQELIDKLKEEAEQHKI   59 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555666677777777777777777666

>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=88.16  E-value=0.85  Score=31.25  Aligned_cols=36  Identities=25%  Similarity=0.364  Sum_probs=19.0

Q ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           35 QSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        35 ~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      .....++.+..+|+.|-..|+.+...|+.|...|.+
T Consensus        36 ~r~~e~~~r~~~L~~eN~~L~~~v~~L~~E~~~Lr~   71 (78)
T 1gu4_A           36 MRNLETQHKVLELTAENERLQKKVEQLSRELSTLRN   71 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444555555555555555555555555555543

>3swk_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural; 1.70A {Homo sapiens}

Probab=87.79  E-value=3.2  Score=28.44  Aligned_cols=25  Identities=16%  Similarity=0.339  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELK   48 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~   48 (136)
                      .+||.|+..+..++..|.-++..+.
T Consensus         3 ~eLr~qi~~l~~e~~~l~~e~dn~~   27 (86)
T 3swk_A            3 RELRRQVDQLTNDKARVEVERDNLA   27 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            4566666666666666655554443

>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=87.59  E-value=0.9  Score=27.52  Aligned_cols=24  Identities=38%  Similarity=0.581  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           39 DLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        39 ~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      .|+++..+|..++++|.+|-.+||
T Consensus         5 QLE~KVEeLl~~~~~Le~eV~RLk   28 (36)
T 1kd8_B            5 QLKAKVEELKSKLWHLKNKVARLK   28 (36)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHH
Confidence            344555555555555555555554

>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=87.44  E-value=3.6  Score=28.40  Aligned_cols=41  Identities=24%  Similarity=0.489  Sum_probs=22.9

Q ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           32 KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +|++.+..-+.|+..|+.=.+||++=++.|+.=+.+|+++-
T Consensus        15 rl~E~~~q~qaEl~sLrrT~~EL~~G~~KL~~mi~~l~~E~   55 (78)
T 3iv1_A           15 RMKEEMDRAQAELNALKRTEEDLKKGHQKLEEMVTRLDQEV   55 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            44555555555555555555555555555555555555543

>1uii_A Geminin; human, DNA replication, cell cycle; 2.00A {Homo sapiens} SCOP: h.1.28.1

Probab=87.37  E-value=1.4  Score=30.86  Aligned_cols=13  Identities=31%  Similarity=0.445  Sum_probs=4.8

Q ss_pred             HHHHHHHhHHHHH
Q 032660           54 LRDEKQRLKADKE   66 (136)
Q Consensus        54 LrdEk~~Lk~eke   66 (136)
                      |++|+..||.+.+
T Consensus        58 l~eEi~~lk~en~   70 (83)
T 1uii_A           58 KDNEIARLKKENK   70 (83)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            3333333333333

>1wlq_A Geminin; coiled-coil; 2.80A {Mus musculus} PDB: 2zxx_A*

Probab=87.28  E-value=2.7  Score=29.48  Aligned_cols=27  Identities=30%  Similarity=0.480  Sum_probs=13.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           36 STEDLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        36 ~n~~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      +|+.|.+++..+..|.+.|++|+..|+
T Consensus        39 EN~~Lh~~ie~~~eEi~~Lk~en~~L~   65 (83)
T 1wlq_A           39 ENEKLHKEIEQKDSEIARLRKENKDLA   65 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444444555555555444

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=87.10  E-value=2.6  Score=44.74  Aligned_cols=39  Identities=15%  Similarity=0.259  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      |-.-|+.++.++++|.++.+.|+++..+...||.+|++|
T Consensus      2026 ~~~~L~~~~~~L~~le~~l~~L~~~~~~~~~ek~~L~~e 2064 (3245)
T 3vkg_A         2026 LKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTE 2064 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444444444444444433

>3trt_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural protein; 2.30A {Homo sapiens} PDB: 3klt_A*

Probab=86.99  E-value=4.4  Score=26.35  Aligned_cols=55  Identities=15%  Similarity=0.290  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHhhHH-----HHHHHHHHHHH-------HHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           21 RMMEQLRTEAQKLKQSTED-----LQEKIKELKAE-------KNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~-----L~ee~~~L~~E-------KnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .+|.++|+|-+.+-..|..     .+.++.+|...       -...++|...|+..+.+|+.+|..+
T Consensus         9 ~il~eiRaQYE~ia~knr~EaE~~y~~k~eel~~~~~~~~~~l~~~k~Ei~elrr~iq~L~~el~sl   75 (77)
T 3trt_A            9 AAMRDVRQQYESVAAKNLQEAEEWYKSKFADLSEAANRNNDALRQAKQESTEYRRQVQSLTMEVDAL   75 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4556677776665544422     22334444433       3334566666777777777776654

>1ic2_A Tropomyosin alpha chain, skeletal muscle; alpha-helical coiled coil, alanine, symmetry, axial stagger, BEND, contractIle protein; 2.00A {Gallus gallus} SCOP: h.1.5.1

Probab=86.65  E-value=5.3  Score=26.62  Aligned_cols=45  Identities=16%  Similarity=0.219  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      ..|+.+.....+....++.+.+........+.+|...|+.-+--|
T Consensus         9 ~~lk~e~d~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~l   53 (81)
T 1ic2_A            9 QMLKLDKENALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGT   53 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            344444444444444444444443333333333333333333333

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=86.64  E-value=4.7  Score=29.25  Aligned_cols=46  Identities=24%  Similarity=0.263  Sum_probs=23.1

Q ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           28 TEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        28 ~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      =||+-||+..+.++|..-.+..|..|...|...+|.....|+.++.
T Consensus        30 YqVdlLKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~   75 (103)
T 4h22_A           30 YQVDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFA   75 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3555555555555555555555544444444444444444444433

>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=86.55  E-value=1.7  Score=30.63  Aligned_cols=21  Identities=38%  Similarity=0.561  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHHH
Q 032660           51 KNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        51 KnELrdEk~~Lk~eke~Le~q   71 (136)
                      +.+|.+|+..|..|++.|..+
T Consensus        50 ~~~LE~e~~~L~~e~~~L~~e   70 (90)
T 2wt7_B           50 KHHLENEKTQLIQQVEQLKQE   70 (90)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444333

>2xv5_A Lamin-A/C; structural protein, intermediate filaments, nuclear membrane LEFT-handed coiled coil, right-handed coiled coil; HET: MSE; 2.40A {Homo sapiens}

Probab=86.47  E-value=4.2  Score=27.40  Aligned_cols=47  Identities=15%  Similarity=0.196  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      ..+++..+..|+++...+..++.....|-.+|.+=|.+|..||.---
T Consensus         7 ~~~~~~~i~~lE~eL~~~r~e~~~ql~EYq~LlniKl~Le~EIatYR   53 (74)
T 2xv5_A            7 RDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYR   53 (74)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45666777777777777777777777777778888888887775443

>2bni_A General control protein GCN4; four helix bundle, antiparallel four helix bundle acyl transferase; HET: TYZ; 1.5A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 2ccn_A 1w5k_A* 2ccf_A 2cce_A 1w5j_A* 1uo2_A 1gcl_A 1uo1_A 1unv_A 1uo0_A 1unt_A 1uo5_A 1unz_A 1unx_A 1unu_A 1unw_A 1uo4_A 1uo3_A 1uny_A 1u9f_A* ...

Probab=86.43  E-value=1.2  Score=26.64  Aligned_cols=26  Identities=19%  Similarity=0.488  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           38 EDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        38 ~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      ..|+++..+|-.++++|.+|-.+||.
T Consensus         4 nQLEdKvEeLl~~~~~L~~EV~RLk~   29 (34)
T 2bni_A            4 KQIEDKLEEILSKGHHICNELARIKK   29 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHccHHHHHHHHHHHH
Confidence            45677777777777777777777764

>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=86.13  E-value=3.8  Score=26.22  Aligned_cols=43  Identities=16%  Similarity=0.280  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      +.+|-++++.|......|.+++..|+       .+-..-|.|-.|-++.|
T Consensus         6 i~~Lss~V~~L~~kVdqLssdV~al~-------~~v~~ak~eA~RAN~Rl   48 (52)
T 1jcd_A            6 ADQASSDAQTANAKADQASNDANAAR-------SDAQAAKDDAARANQRA   48 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHhh
Confidence            45566666666666666666555544       44445555555554443

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=86.01  E-value=7.6  Score=27.76  Aligned_cols=55  Identities=16%  Similarity=0.286  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 032660           18 DVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQV   72 (136)
Q Consensus        18 DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~ql   72 (136)
                      ++=.=+.+|.++......+...|.++..+-..-+-+...++..+..|.|.|-..|
T Consensus         9 ~lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLTasL   63 (97)
T 2eqb_B            9 QLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASL   63 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344466667777777777777776666666666666666666666666665544

>1uo4_A General control protein GCN4; four helix bundle, cavity, iodobenzene; 1.70A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 1uo3_A 1unt_A 1uo5_A 1unu_A 1unv_A 1uo1_A 2ccf_A 2cce_A 1unx_A 1unw_A 1w5j_A* 1w5k_A* 1u9f_A* 3f86_A* 3f87_A* 3hez_A* 3c3f_A*

Probab=85.94  E-value=1.3  Score=26.46  Aligned_cols=25  Identities=20%  Similarity=0.381  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           39 DLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        39 ~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      .|+++..+|-.++.+|++|-.+||.
T Consensus         5 QLEdKVEeLl~~n~~Le~EV~RLk~   29 (34)
T 1uo4_A            5 QIEDKGEEILSKLYHIENELARIKK   29 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            4556666666666666666666653

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=85.79  E-value=5.8  Score=28.74  Aligned_cols=52  Identities=12%  Similarity=0.202  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |.=|+..++.+.+.+..++-+.++...|.+-++-....|+.+...|..||+.
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            4446677888889999999999999999999999999999999999999987

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=85.38  E-value=3.5  Score=26.13  Aligned_cols=30  Identities=23%  Similarity=0.351  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKIKELKAE   50 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~~~L~~E   50 (136)
                      .|+.+|..++..|..+|..|..++..|+.+
T Consensus        22 ~~~~~LE~~v~~L~~eN~~L~~~~~~L~~~   51 (55)
T 1dh3_A           22 EYVKSLENRVAVLENQNKTLIEELKALKDL   51 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            466777777777777777777766666544

>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=85.38  E-value=7.3  Score=26.98  Aligned_cols=15  Identities=27%  Similarity=0.315  Sum_probs=5.5

Q ss_pred             HHHHHHHhhHHHHHH
Q 032660           29 EAQKLKQSTEDLQEK   43 (136)
Q Consensus        29 e~~~Lk~~n~~L~ee   43 (136)
                      |++.|-.+|..|.+.
T Consensus        10 evEnLi~EN~eLl~T   24 (77)
T 2w83_C           10 EVENLILENTQLLET   24 (77)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            333333333333333

>1ik9_A DNA repair protein XRCC4; DNA END joining, double-strand break repair, V(D)J recombination, protein-protein complex, coiled coil; HET: DNA; 2.30A {Homo sapiens} SCOP: b.59.1.1 h.1.11.1 PDB: 3ii6_A* 1fu1_A* 3rwr_A*

Probab=85.37  E-value=4.5  Score=31.89  Aligned_cols=49  Identities=18%  Similarity=0.226  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      +.-+-..+..|+.+|..|+++...|..+-|+|.++.-.+-.+|+++|.+
T Consensus       127 fd~~~~~~~~~~~~~~~L~~e~~~l~~~~~~l~~qlE~~v~~K~~~E~~  175 (213)
T 1ik9_A          127 IAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETD  175 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333444444444444444444444444444444444444444443

>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=85.17  E-value=2.1  Score=25.92  Aligned_cols=26  Identities=27%  Similarity=0.514  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHH
Q 032660           39 DLQEKIKELKAEKNELRDEKQRLKAD   64 (136)
Q Consensus        39 ~L~ee~~~L~~EKnELrdEk~~Lk~e   64 (136)
                      .|+++..+|-.+|++|.+|-.+|+..
T Consensus         5 QLE~kVEeLl~~~~~Le~EV~RL~~l   30 (36)
T 1kd8_A            5 QLEAEVEEIESEVWHLENEVARLEKE   30 (36)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            45555666666666666666666543

>3w03_C DNA repair protein XRCC4; coiled-coil, NHEJ, DSBS repair, KU70/80, DNA-PKCS, DNA ligas binding protein; HET: DNA; 8.49A {Homo sapiens}

Probab=85.11  E-value=2.1  Score=33.68  Aligned_cols=40  Identities=18%  Similarity=0.278  Sum_probs=27.4

Q ss_pred             HHHHH-HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 032660           17 SDVVR-MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRD   56 (136)
Q Consensus        17 ~DAir-~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrd   56 (136)
                      .++|+ ++.-+-..++.|+++|..|+++...|..|-|+..+
T Consensus       140 ~e~i~elid~~ld~~~~L~~~n~~LqkeNeRL~~E~n~~l~  180 (184)
T 3w03_C          140 AEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQG  180 (184)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555 66777777777777777777777777766665544

>1a93_B MAX protein, coiled coil, LZ; leucine zipper, 2D solution structure, H-bonds, buried salt bridge, proto-oncogene, nuclear protein; NMR {Mus musculus} SCOP: h.1.3.1 PDB: 2a93_B

Probab=85.00  E-value=0.8  Score=27.42  Aligned_cols=18  Identities=17%  Similarity=0.434  Sum_probs=7.1

Q ss_pred             HHHHHHHHhhHHHHHHHH
Q 032660           28 TEAQKLKQSTEDLQEKIK   45 (136)
Q Consensus        28 ~e~~~Lk~~n~~L~ee~~   45 (136)
                      .+|+.||..|..|+++++
T Consensus        14 qDIddlkrQN~~Le~Qir   31 (34)
T 1a93_B           14 QDIDDLKRQNALLEQQVR   31 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHH
Confidence            333444444444443333

>3oa7_A Head morphogenesis protein, chaotic nuclear migra protein 67 fusion protein; coiled coils, structural protein, spindle POLE BODY; 2.30A {Bacillus phage PHI29}

Probab=84.87  E-value=2.4  Score=34.13  Aligned_cols=43  Identities=21%  Similarity=0.298  Sum_probs=39.4

Q ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           29 EAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        29 e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      -.|.|+++..+.-++..+|+..-++|+.|+..|+....+|+.-
T Consensus        31 ~~~~~~a~~~s~~s~~~dl~~s~~~l~ae~~~L~~~l~kLeGn   73 (206)
T 3oa7_A           31 ALQQLRVNYGSFVSEYNDLTKSHNTLSKELDNLRSRFGNLEGN   73 (206)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHccCC
Confidence            3689999999999999999999999999999999999999853

>3u1c_A Tropomyosin alpha-1 chain; anti-parallel coiled coil, contractIle protein; 1.80A {Gallus gallus} PDB: 3u1a_A

Probab=84.80  E-value=8  Score=26.94  Aligned_cols=24  Identities=21%  Similarity=0.439  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKEL   47 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L   47 (136)
                      .++..++..+...+..+.+++.+|
T Consensus        26 e~~e~~~k~~e~~~~~~E~Ei~sL   49 (101)
T 3u1c_A           26 EQAEADKKAAEERSKQLEDDIVQL   49 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHH
Confidence            333333333333333333333333

>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=84.69  E-value=2.4  Score=35.60  Aligned_cols=49  Identities=18%  Similarity=0.135  Sum_probs=39.3

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ....++|.++...|+..+.....+...|+.....+++.|.+|+++|..+
T Consensus         4 ~~~~~~~~~~~~~~e~~i~~~~~~i~~L~~~l~~~~~~i~~l~~~i~~l   52 (323)
T 1lwu_C            4 QKTVQKILEEVRILEQIGVSHDAQIQELSEMWRVNQQFVTRLQQQLVDI   52 (323)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456788888888888888888888888888888888888888877664

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=84.57  E-value=2.1  Score=29.05  Aligned_cols=46  Identities=11%  Similarity=0.200  Sum_probs=31.5

Q ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           30 AQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        30 ~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      ...|.+.+..|+.++-+...-.++|-+.-.....+|++|+.|++.+
T Consensus         9 ~~~le~Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L   54 (78)
T 3efg_A            9 DQELEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHL   54 (78)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455666666666666666666677777777777777777777765

>2zxx_A Geminin; coiled-coil, cell cycle, coiled coil, DNA replication inhibitor, phosphoprotein, DNA-binding, nucleus, proto-oncogene; HET: DNA; 2.80A {Mus musculus}

Probab=84.56  E-value=2.3  Score=29.47  Aligned_cols=28  Identities=29%  Similarity=0.463  Sum_probs=14.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           36 STEDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        36 ~n~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      +|..|-.++..++.|.+.|++|+..|+.
T Consensus        35 EN~~Lh~~ie~~~eEi~~LkeEN~~L~e   62 (79)
T 2zxx_A           35 ENEKLHKEIEQKDSEIARLRKENKDLAE   62 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444555555555555555555543

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.56  E-value=1.6  Score=37.43  Aligned_cols=46  Identities=20%  Similarity=0.308  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      .+|..++++|..++.-|+.+..+++.|.+.|+.|...++.|+.+|+
T Consensus        45 ~dl~~~lk~le~~~~~L~~e~e~l~~~~~~~~~e~~~~~ee~~~l~   90 (428)
T 4b4t_K           45 SDIYFKLKKLEKEYELLTLQEDYIKDEQRHLKRELKRAQEEVKRIQ   90 (428)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            3555555556666666666666666666666666666666666554

>1gk4_A Vimentin; intermediate filament, dimer, parallel coiled coil, heptad repeat, stutter; 2.3A {Homo sapiens} SCOP: h.1.20.1

Probab=84.47  E-value=7.3  Score=26.23  Aligned_cols=30  Identities=17%  Similarity=0.264  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           45 KELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        45 ~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.+....++|..+.+.++.+.++.-++++.
T Consensus        29 ~~~q~~i~~lE~eL~~~r~e~~~q~~EYq~   58 (84)
T 1gk4_A           29 ANYQDTIGRLQDEIQNMKEEMARHLREYQD   58 (84)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334445556666777777777666666655

>2hy6_A General control protein GCN4; protein design, parallel heptamer, protein structure, biosyn protein; 1.25A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 2nrn_A 3crp_A 2b1f_A 3crp_B 2ipz_A 3ck4_A 3ck4_B 2b22_A 1ce9_A

Probab=84.41  E-value=1.7  Score=25.95  Aligned_cols=25  Identities=24%  Similarity=0.415  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           39 DLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        39 ~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      .|+++..+|-.++++|.+|-.+|+.
T Consensus         5 QLEdkVEeLl~~~~~Le~eV~RL~~   29 (34)
T 2hy6_A            5 QLADAVEELASANYHLANAVARLAK   29 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            4566666666666666666666653

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=84.39  E-value=2.1  Score=36.26  Aligned_cols=55  Identities=16%  Similarity=0.256  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      -.=++.|+.+.++|+++++.++.+.++|+.+-.+...+...|..++..|...++-
T Consensus         9 ~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~rr~l~n~~~elkgnIrV   63 (403)
T 4etp_A            9 KEKIAALKEKIAALKEKIKDTELGMKELNEILIKEETVRRTLHNELQELRGNIRV   63 (403)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEE
Confidence            3457788899999999999999999999887777777777787777777666555

>2zxx_A Geminin; coiled-coil, cell cycle, coiled coil, DNA replication inhibitor, phosphoprotein, DNA-binding, nucleus, proto-oncogene; HET: DNA; 2.80A {Mus musculus}

Probab=84.35  E-value=4.3  Score=28.11  Aligned_cols=34  Identities=21%  Similarity=0.330  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKA   49 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~   49 (136)
                      |.||..==++|..++..+++++..|+++++.|+.
T Consensus        29 L~eaL~EN~~Lh~~ie~~~eEi~~LkeEN~~L~e   62 (79)
T 2zxx_A           29 LYEALKENEKLHKEIEQKDSEIARLRKENKDLAE   62 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5666666666666666666666666666666643

>3ibp_A Chromosome partition protein MUKB; structural maintenance of chromosomes, SMC, condensin, chromosome segregation, hinge, dimerization domain; 3.10A {Escherichia coli}

Probab=84.29  E-value=4.9  Score=33.94  Aligned_cols=26  Identities=27%  Similarity=0.456  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           45 KELKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        45 ~~L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      ++++.+++++-.+|..|..+|++|-+
T Consensus        79 re~~~~Rd~~a~~k~~Le~~ierLs~  104 (302)
T 3ibp_A           79 REAIVERDEVGARKNAVDEEIERLSQ  104 (302)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            67777777777777777777777654

>2ve7_A Kinetochore protein HEC1, kinetochore protein SPC; mitosis, centromere, cell cycle, microtubule, C division, calponin homology; 2.88A {Homo sapiens} PDB: 3iz0_C*

Probab=84.18  E-value=2.3  Score=34.94  Aligned_cols=29  Identities=21%  Similarity=0.381  Sum_probs=18.5

Q ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           29 EAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        29 e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      |++.|++++..|++++.+|+.+++.++..
T Consensus       186 eie~L~~~~~~L~eEi~~Le~~~e~~~k~  214 (315)
T 2ve7_A          186 KLESLEAKNRALNEQIARLEQERSTANKA  214 (315)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            66666666666666666666666555553

>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=84.12  E-value=7.3  Score=25.95  Aligned_cols=26  Identities=12%  Similarity=0.360  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHH
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAE   50 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~E   50 (136)
                      ++..++......+..+.+++..|+..
T Consensus        24 ~~e~~l~~~e~~~~~~E~ev~~L~kK   49 (81)
T 1ic2_A           24 QAEADKKAAEERSKQLEDELVALQKK   49 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            33333333333444444444444433

>2wg5_A General control protein GCN4, proteasome-activating nucleotidase; transcription hydrolase complex, nucleotide-binding; 2.10A {Saccharomyces cerevisiae} PDB: 2wg6_A

Probab=83.87  E-value=1  Score=31.98  Aligned_cols=26  Identities=27%  Similarity=0.475  Sum_probs=13.7

Q ss_pred             HHHHHHHhHHHHHHHHHHHHhccCCC
Q 032660           54 LRDEKQRLKADKEKLEQQVKAMSAPS   79 (136)
Q Consensus        54 LrdEk~~Lk~eke~Le~qlk~~~~~p   79 (136)
                      |+++...|+.++++++.+++.+..+|
T Consensus        12 l~~~~~~l~~~i~~lkeel~~L~~~P   37 (109)
T 2wg5_A           12 LEDKVEELLSKNYHLENEVARLRSPP   37 (109)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            33444444455555555566655555

>2zvf_A Alanyl-tRNA synthetase; C-terminal, oligomerization domain, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase, nucleotide-binding; 3.20A {Archaeoglobus fulgidus}

Probab=83.85  E-value=3  Score=30.26  Aligned_cols=50  Identities=18%  Similarity=0.274  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHHh----hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           19 VVRMMEQLRTEAQKLKQS----TEDLQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~----n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      |++++.+....+.++...    ...+.+.+..|..|..+|+.|...|+.++...
T Consensus         5 A~~~~~~~~~~l~~~a~~Lk~~~~~l~~~v~~l~~e~k~l~ke~~~l~~~~a~~   58 (171)
T 2zvf_A            5 AIEAVEEMERLLREASSILRVEPAKLPKTVERFFEEWKDQRKEIERLKSVIADL   58 (171)
T ss_dssp             GTHHHHHHHHHHHHHHHTTTCCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344554444444443332    23555555555555555555555555554443

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=83.85  E-value=8.4  Score=26.45  Aligned_cols=43  Identities=14%  Similarity=0.321  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKAD   64 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~e   64 (136)
                      .+-+|..+++.|+.++..|+-.+.++.-+.+.|...-..+-.+
T Consensus        21 ~~~~Lq~Ql~~Lq~Ev~~LRGqiE~~~~~l~ql~~rQrd~Y~d   63 (83)
T 2xdj_A           21 LLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQ   63 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555555555555555555554444444444443333333

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=83.83  E-value=4.3  Score=29.11  Aligned_cols=58  Identities=9%  Similarity=0.249  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH----HHHhHHHHHHHHHHHHh
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE----KQRLKADKEKLEQQVKA   74 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE----k~~Lk~eke~Le~qlk~   74 (136)
                      ..+=.-+++||..++.|..++.+|......|.....|++..    ...+...+..||.+|..
T Consensus        32 ~~~k~Ei~elrr~iq~L~~el~~l~~~~~~LE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~   93 (129)
T 3tnu_B           32 RNTKHEISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQRGELALKDARNKLAELEEALQK   93 (129)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence            33445688889999999999999988888888888887654    33556666667666654

>1s1c_X RHO-associated, coiled-coil containing protein kinase 1; GTPase, RHO kinase, ROCK, signaling protein; HET: GNP; 2.60A {Homo sapiens} SCOP: h.1.27.1

Probab=83.71  E-value=7.1  Score=26.49  Aligned_cols=48  Identities=23%  Similarity=0.369  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           25 QLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        25 qLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      .|...++-|..+++.|....+.+..|..-+++|-..  +.+.+++.+|+.
T Consensus         3 ~L~k~i~~l~~E~eel~~klk~~~ee~~~~~eee~~--~~~~~lek~L~~   50 (71)
T 1s1c_X            3 MLTKDIEILRRENEELTEKMKKAEEEYKLEKEEEIS--NLKAAFEKNINT   50 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--THHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Confidence            355556666666666666666665555555544433  444455555543

>2dq3_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, nationa on protein structural and functional analyses; HET: SSA; 3.00A {Aquifex aeolicus}

Probab=83.67  E-value=2.6  Score=35.83  Aligned_cols=53  Identities=23%  Similarity=0.433  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHH----------HHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIK----------ELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~----------~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      -++|+.+++.|+++...+..+|.          +|+.|..+|+++...|+.+...++.++..+
T Consensus        39 ~r~~~~~~~~l~~~~n~~sk~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (425)
T 2dq3_A           39 RREIIKRLEALRSERNKLSKEIGKLKREGKDTTEIQNRVKELKEEIDRLEEELRKVEEELKNT  101 (425)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTGGGSSCSCTTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhcCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35666777777777777777765          345566666777777777777777777663

>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=83.46  E-value=4.4  Score=27.67  Aligned_cols=29  Identities=31%  Similarity=0.487  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 032660           40 LQEKIKELKAEKNELRDEKQRLKADKEKL   68 (136)
Q Consensus        40 L~ee~~~L~~EKnELrdEk~~Lk~eke~L   68 (136)
                      |+++.+.+..++++|+.++..|+.+++.|
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            33333444444555555555555555544

>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=83.22  E-value=2.4  Score=38.45  Aligned_cols=43  Identities=23%  Similarity=0.315  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKE   66 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke   66 (136)
                      .+||..++.||+++..-...|+-|..-..++|.+.++|+.+|+
T Consensus       113 ~ELRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvDId  155 (562)
T 3ghg_A          113 EDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDID  155 (562)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3899999999998888779999999999999999999998874

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=83.14  E-value=8.2  Score=26.49  Aligned_cols=39  Identities=15%  Similarity=0.250  Sum_probs=21.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           36 STEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        36 ~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ..-.|+..+..|..|..+||-....+.-+++.+.++-+.
T Consensus        21 ~~~~Lq~Ql~~Lq~Ev~~LRGqiE~~~~~l~ql~~rQrd   59 (83)
T 2xdj_A           21 LLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQ   59 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555555555555555554443

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=83.12  E-value=5.5  Score=29.17  Aligned_cols=33  Identities=30%  Similarity=0.421  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR   55 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELr   55 (136)
                      +..|..++....+....-+.++.+|+.|.-.++
T Consensus        26 i~~L~~~L~~AEeaL~~Kq~~idelk~ei~q~~   58 (110)
T 2v4h_A           26 LEDLRQQLQQAEEALVAKQELIDKLKEEAEQHK   58 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555555555555555555555555444433

>3he4_B Synzip5; heterodimeric coiled-coil, de novo protein; 2.46A {Artificial gene}

Probab=83.08  E-value=5.5  Score=24.80  Aligned_cols=35  Identities=29%  Similarity=0.389  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE   57 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE   57 (136)
                      ||.|..=+|+|.+.|..|..--.-|+--|.||.=|
T Consensus         5 vkelknyiqeleernaelknlkehlkfakaelefe   39 (46)
T 3he4_B            5 VKELKNYIQELEERNAELKNLKEHLKFAKAELEFE   39 (46)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHHHHhHHHHHHHHHHHHHHH
Confidence            56777777777777766554444444444444433

>1l8d_A DNA double-strand break repair RAD50 ATPase; zinc finger, DNA repair, recombination, HOOK motif, replication; HET: DNA CIT; 2.20A {Pyrococcus furiosus} SCOP: h.4.12.1

Probab=83.03  E-value=4.4  Score=27.69  Aligned_cols=31  Identities=19%  Similarity=0.386  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           43 KIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        43 e~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +++++..+..+|+++...|+.+++.|+.++.
T Consensus        72 ~l~~l~~~i~~l~~~i~~l~~~~~~l~~~~~  102 (112)
T 1l8d_A           72 DLNNSKNTLAKLIDRKSELERELRRIDMEIK  102 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444445555544444

>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=82.93  E-value=2.8  Score=35.80  Aligned_cols=52  Identities=15%  Similarity=0.268  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |..|+.+.++|+.++..++++.++++.+..+...+...|..++..|...++-
T Consensus        12 l~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~rr~l~n~~~~l~gnIrV   63 (412)
T 3u06_A           12 VVHLRQRTEELLRCNEQQAAELETCKEQLFQSNMERKELHNTVMDLRDNIRV   63 (412)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCEEE
Confidence            5566777777777777777777777766666555666666666665554444

>4dzn_A Coiled-coil peptide CC-PIL; de novo protein; HET: PHI; 1.59A {Synthetic} PDB: 4dzm_A* 4dzl_A* 4dzk_A 1u0i_A 1u0i_B

Probab=82.79  E-value=2.8  Score=24.59  Aligned_cols=14  Identities=29%  Similarity=0.311  Sum_probs=5.4

Q ss_pred             HHHHHHhHHHHHHH
Q 032660           55 RDEKQRLKADKEKL   68 (136)
Q Consensus        55 rdEk~~Lk~eke~L   68 (136)
                      +.|...||-||.-|
T Consensus        15 kkeiaalkfeiaal   28 (33)
T 4dzn_A           15 KKEIAALKFEIAAL   28 (33)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333344443333

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=82.76  E-value=5  Score=28.90  Aligned_cols=56  Identities=14%  Similarity=0.146  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH----HHHhHHHHHHHHHHHHh
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDE----KQRLKADKEKLEQQVKA   74 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdE----k~~Lk~eke~Le~qlk~   74 (136)
                      +=.-+++||..++.|..++.++......|.....|++..    ...+...+..||.+|..
T Consensus        36 ~k~Ei~elrr~iq~L~~el~~l~~~~~sLE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~   95 (131)
T 3tnu_A           36 GKSEISELRRTMQNLEIELQSQLSMKASLENSLEETKGRYCMQLAQIQEMIGSVEEQLAQ   95 (131)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344577888888888888888888888888777777653    33455566666666654

>4aj5_1 SKA3, spindle and kinetochore-associated protein 3; cell cycle, SKA complex, mitosis, cell division, kinetochore microtubule attachment; 3.32A {Homo sapiens}

Probab=82.73  E-value=10  Score=27.37  Aligned_cols=57  Identities=19%  Similarity=0.239  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH----HHhHHHHHHHHHHHH
Q 032660           17 SDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEK----QRLKADKEKLEQQVK   73 (136)
Q Consensus        17 ~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk----~~Lk~eke~Le~qlk   73 (136)
                      .-+.|+|.||.+||.-||.....+..+.+.=.+|-++--..-    .+...+|.+|..-++
T Consensus        38 ~~~~rilhdl~seV~~LK~dv~~~L~k~~~e~qe~~~FIKa~kvL~~rns~DI~~ire~fq   98 (101)
T 4aj5_1           38 DYPMRILYDLHSEVQTLKDDINILLDKARLENQEGIDFIKATKVLMEKNSMDIMKIREYFQ   98 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            347899999999999999998888887665555544433322    233456666665443

>3rrk_A V-type ATPase 116 kDa subunit; alpha beta fold, proton pump, subunit I/A, V-ATPase, proton; HET: NHE; 2.64A {Meiothermus ruber}

Probab=82.71  E-value=3.1  Score=33.44  Aligned_cols=33  Identities=12%  Similarity=0.272  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           39 DLQEKIKELKAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        39 ~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      .+++.+..+..+-++|.+++..|++++++|+.+
T Consensus        96 ~~e~~~~~l~~~~~~l~~~~~~L~~~~~~l~~~  128 (357)
T 3rrk_A           96 EAEAVLRPVASRAEVLGKERAALEEEIQTIELF  128 (357)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            344445555555555555555555555555555

>1dip_A Delta-sleep-inducing peptide immunoreactive peptide; structure, leucine zipper, PIG, acetylation; NMR {Sus scrofa} SCOP: h.1.12.1

Probab=82.48  E-value=1.2  Score=31.07  Aligned_cols=28  Identities=36%  Similarity=0.500  Sum_probs=14.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           36 STEDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        36 ~n~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      +.+-|.+.|++|...-++|+-||+.||.
T Consensus        16 EVevLKe~I~EL~e~~~qLE~EN~~Lk~   43 (78)
T 1dip_A           16 EVEILKEQIRELVEKNSQLERENTLLKT   43 (78)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444555555555555566665553

>3m48_A General control protein GCN4; leucine zipper, synthetic peptide, alpha helix, activa amino-acid biosynthesis, DNA-binding, nucleus; 1.45A {Synthetic} PDB: 3i1g_A 2ahp_A* 2o7h_A

Probab=82.38  E-value=1.7  Score=25.82  Aligned_cols=24  Identities=25%  Similarity=0.401  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHH
Q 032660           47 LKAEKNELRDEKQRLKADKEKLEQ   70 (136)
Q Consensus        47 L~~EKnELrdEk~~Lk~eke~Le~   70 (136)
                      |...-.||..||+.|+.|.+||..
T Consensus         5 LE~kVEeLl~~n~~Le~EV~RLk~   28 (33)
T 3m48_A            5 LEAKVEELLSKNWNLENEVARLKK   28 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHH
Confidence            444445555555555555555543

>2zqm_A Prefoldin beta subunit 1; chaperone; HET: CIT; 1.90A {Thermococcus SP} PDB: 2zdi_A

Probab=82.37  E-value=5.2  Score=27.23  Aligned_cols=31  Identities=23%  Similarity=0.446  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           44 IKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        44 ~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.++..+...|......+..+.++++.+|+.
T Consensus        79 ~e~ie~~i~~le~~~~~l~~~l~~lk~~l~~  109 (117)
T 2zqm_A           79 IETLEVRLNALERQEKKLNEKLKELTAQIQS  109 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333344444444444444444455555554

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=82.29  E-value=10  Score=26.20  Aligned_cols=32  Identities=16%  Similarity=0.289  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAEK   51 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EK   51 (136)
                      +.-..++..++..+...+..+.+++..|+...
T Consensus        22 ~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKi   53 (101)
T 3u59_A           22 IDRAEQAEADKKQAEDRCKQLEEEQQGLQKKL   53 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            33334444444444444444444444444333

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=82.26  E-value=6.6  Score=26.74  Aligned_cols=45  Identities=16%  Similarity=0.189  Sum_probs=28.4

Q ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           30 AQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        30 ~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      +.+|+.....-.++++....-..+|..+......+|.+|+.+|.-
T Consensus        21 i~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDK   65 (72)
T 3nmd_A           21 LRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDK   65 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666666666666666666666666666666666666644

>1wt6_A Myotonin-protein kinase; coiled-coil, kinase activation, DMPK, molecular replacement, transferase; 1.60A {Homo sapiens}

Probab=82.08  E-value=6.5  Score=27.43  Aligned_cols=55  Identities=16%  Similarity=0.328  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHH---HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           21 RMMEQLRTEAQ---KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        21 r~lkqLr~e~~---~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .+-.-|.+||+   .+.++....++.+.....+..|-...+..|..|+++|+.+++.+
T Consensus        14 eLQSALeaEIqAKQ~i~EELs~vr~~ni~~eskL~eae~rn~eL~~e~~~l~~~~eel   71 (81)
T 1wt6_A           14 ELQEALEEEVLTRQSLSREMEAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMELL   71 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445666663   46667777777777888888888889999999999999999885

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.06  E-value=1.5  Score=37.75  Aligned_cols=48  Identities=15%  Similarity=0.243  Sum_probs=22.6

Q ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCCC
Q 032660           32 KLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAMSAPS   79 (136)
Q Consensus        32 ~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~~~~p   79 (136)
                      +|+.....|+.+++.|+.|..-+..|+..++.++.+++.+++.+..+|
T Consensus        29 ~l~~r~~~le~e~~~l~~e~~r~~~e~~~~~~~~~~~~~~i~~~~~~p   76 (434)
T 4b4t_M           29 ELQTRAKLLDNEIRIFRSELQRLSHENNVMLEKIKDNKEKIKNNRQLP   76 (434)
T ss_dssp             ------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCc
Confidence            344444455556666666666666666666666666666666655544

>3lss_A Seryl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, serrs, translation, ATP-binding, nucleotide-binding, structural genomics; HET: ATP; 1.95A {Trypanosoma brucei} PDB: 3lsq_A*

Probab=82.02  E-value=8.5  Score=33.83  Aligned_cols=25  Identities=8%  Similarity=-0.016  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHH
Q 032660           24 EQLRTEAQKLKQSTEDLQEKIKELK   48 (136)
Q Consensus        24 kqLr~e~~~Lk~~n~~L~ee~~~L~   48 (136)
                      +.|+.+++.|+++...+..+|..++
T Consensus        47 r~~~~~~~~l~~~rN~~sk~i~~~~   71 (484)
T 3lss_A           47 RRTQFLTEASKKLINICSKAVGAKK   71 (484)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4556666666666666665554433

>3lss_A Seryl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, serrs, translation, ATP-binding, nucleotide-binding, structural genomics; HET: ATP; 1.95A {Trypanosoma brucei} PDB: 3lsq_A*

Probab=81.87  E-value=6.8  Score=34.42  Aligned_cols=56  Identities=13%  Similarity=0.237  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHH---------------------------HHHHH----HHH-HHHHHHHHHHhHHHHHH
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQE---------------------------KIKEL----KAE-KNELRDEKQRLKADKEK   67 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~e---------------------------e~~~L----~~E-KnELrdEk~~Lk~eke~   67 (136)
                      ..-+.+||++.+.+.+++..+..                           +...|    .+| ..+|+++...|+.+...
T Consensus        50 ~~~~~~l~~~rN~~sk~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~i~~le~~~~~  129 (484)
T 3lss_A           50 QFLTEASKKLINICSKAVGAKKKAKEADGDTSEIPPQVKEAYENGTLKGEQVEQLCVLQLKQLSKDLSDQVAGLAKEAQQ  129 (484)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCC----------------------------CHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccchhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556667666666666554422                           34556    666 77777888888888888


Q ss_pred             HHHHHHhc
Q 032660           68 LEQQVKAM   75 (136)
Q Consensus        68 Le~qlk~~   75 (136)
                      ++.++..+
T Consensus       130 ~~~~~~~~  137 (484)
T 3lss_A          130 LEEERDKL  137 (484)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88888764

>3rrk_A V-type ATPase 116 kDa subunit; alpha beta fold, proton pump, subunit I/A, V-ATPase, proton; HET: NHE; 2.64A {Meiothermus ruber}

Probab=80.79  E-value=10  Score=30.45  Aligned_cols=55  Identities=13%  Similarity=0.170  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH-HHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           20 VRMMEQLRTEAQKLKQSTEDLQEKIKELKAE-KNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        20 ir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~E-KnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      -..+.+|..+++.|+.+.+.++.+++.+..+ ...|..=...++.++++.+..-+.
T Consensus       225 ~~~l~~l~~~i~~l~~~l~~~~~~l~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~  280 (357)
T 3rrk_A          225 GKAAARMKERARLAPEELVGIREEVARLSRESGEALIALWTRAKDEVARYKAVADM  280 (357)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4567788889999999888888888888887 777777777777777777665433

>3ni0_A Bone marrow stromal antigen 2; coiled-coil, antiviral defense, immune system, GPI anchor; 1.60A {Mus musculus}

Probab=80.75  E-value=14  Score=26.70  Aligned_cols=60  Identities=20%  Similarity=0.263  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           16 LSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        16 L~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      |+-|-..|.+-..|+.--....++|.++.+.-++.--+-..+-..|+.||..|+++|+-.
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            344445555555555555555666665544333332222344566777788888877763

>2zqm_A Prefoldin beta subunit 1; chaperone; HET: CIT; 1.90A {Thermococcus SP} PDB: 2zdi_A

Probab=80.70  E-value=7.3  Score=26.47  Aligned_cols=24  Identities=21%  Similarity=0.310  Sum_probs=8.9

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHH
Q 032660           48 KAEKNELRDEKQRLKADKEKLEQQ   71 (136)
Q Consensus        48 ~~EKnELrdEk~~Lk~eke~Le~q   71 (136)
                      +..+..+..+...|...++.++.+
T Consensus        76 ~~~~e~ie~~i~~le~~~~~l~~~   99 (117)
T 2zqm_A           76 KEKIETLEVRLNALERQEKKLNEK   99 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333

>3a7o_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.50A {Saccharomyces cerevisiae}

Probab=80.66  E-value=6.6  Score=27.06  Aligned_cols=6  Identities=33%  Similarity=0.407  Sum_probs=2.2

Q ss_pred             HHHHHH
Q 032660           24 EQLRTE   29 (136)
Q Consensus        24 kqLr~e   29 (136)
                      +-||++
T Consensus        21 ~~Lr~e   26 (75)
T 3a7o_A           21 AILQKE   26 (75)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            333333

>2wvr_A Geminin; DNA replication license, DNA replication inhibitor, phosphoprotein, UBL conjugation, DNA-binding, polymorphism; HET: DNA; 3.30A {Homo sapiens}

Probab=80.55  E-value=8.2  Score=31.07  Aligned_cols=35  Identities=23%  Similarity=0.401  Sum_probs=20.0

Q ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 032660           35 QSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLE   69 (136)
Q Consensus        35 ~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le   69 (136)
                      ++|+.|.+++..|..|.+.|++|+..|+.=.+.++
T Consensus       115 eEN~~Lh~~ie~l~eEi~~LkeEn~eLkeLae~~q  149 (209)
T 2wvr_A          115 KENEKLHKEIEQKDNEIARLKKENKELAEVAEHVQ  149 (209)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35555555566666666666666666655444444

>2wvr_A Geminin; DNA replication license, DNA replication inhibitor, phosphoprotein, UBL conjugation, DNA-binding, polymorphism; HET: DNA; 3.30A {Homo sapiens}

Probab=80.52  E-value=3.3  Score=33.34  Aligned_cols=41  Identities=32%  Similarity=0.418  Sum_probs=17.4

Q ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHH---HHHHHhHHHHHHH
Q 032660           28 TEAQKLKQSTEDLQEKIKELKAEKNELR---DEKQRLKADKEKL   68 (136)
Q Consensus        28 ~e~~~Lk~~n~~L~ee~~~L~~EKnELr---dEk~~Lk~eke~L   68 (136)
                      .|.++|.++++.|+++|..|+.|-.+|+   +.-+.|-.=|++|
T Consensus       115 eEN~~Lh~~ie~l~eEi~~LkeEn~eLkeLae~~q~la~vi~~l  158 (209)
T 2wvr_A          115 KENEKLHKEIEQKDNEIARLKKENKELAEVAEHVQYMAELIERL  158 (209)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444433333   3333444444443

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=80.48  E-value=2.4  Score=36.37  Aligned_cols=41  Identities=20%  Similarity=0.319  Sum_probs=27.0

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 032660           27 RTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEK   67 (136)
Q Consensus        27 r~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~   67 (136)
                      ..++++++.....+.+.++.|..++|+|.++...++.|+.+
T Consensus        24 ~~~i~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~e~~~   64 (405)
T 4b4t_J           24 EQKIQETELKIRSKTENVRRLEAQRNALNDKVRFIKDELRL   64 (405)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34566677777777777777777777777665555554443

>4aj5_K Spindle and kinetochore-associated protein 2; cell cycle, SKA complex, mitosis, cell division, kinetochore microtubule attachment; 3.32A {Homo sapiens}

Probab=80.43  E-value=9.9  Score=28.33  Aligned_cols=49  Identities=16%  Similarity=0.192  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           26 LRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        26 Lr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |-.++...|+++..|-...+.+.+|+.|+.|....--...-++-|+++.
T Consensus        48 Ll~~LsaIk~ry~~L~~q~~~iaaeQke~~d~ir~tL~~tm~miQ~LQ~   96 (123)
T 4aj5_K           48 LLKELSVIKSRYQTLYARFKPVAVEQKESKSRICATVKKTMNMIQKLQK   96 (123)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5567788999999999999999999999999988777777777777776

>1uii_A Geminin; human, DNA replication, cell cycle; 2.00A {Homo sapiens} SCOP: h.1.28.1

Probab=80.11  E-value=4.6  Score=28.28  Aligned_cols=28  Identities=25%  Similarity=0.431  Sum_probs=13.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 032660           36 STEDLQEKIKELKAEKNELRDEKQRLKA   63 (136)
Q Consensus        36 ~n~~L~ee~~~L~~EKnELrdEk~~Lk~   63 (136)
                      +|+.|.+.+..|+.|.+.|+.|+..|+.
T Consensus        47 EN~~Lh~~ie~l~eEi~~lk~en~eL~e   74 (83)
T 1uii_A           47 ENEKLHKEIEQKDNEIARLKKENKELAE   74 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444455554443

>1kd8_B GABH BLL, GCN4 acid base heterodimer base-D12LA16L; coiled coil heterodimer, de novo protein; 1.90A {Synthetic} SCOP: h.1.3.1 PDB: 1kd9_B 1kdd_B

Probab=80.07  E-value=5.2  Score=24.15  Aligned_cols=26  Identities=31%  Similarity=0.504  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELK   48 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~   48 (136)
                      ++||...+++|..++..|+.+...|+
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            56777777777777777776665554

>1kd8_A GABH AIV, GCN4 acid base heterodimer acid-D12IA16V; coiled coil heterodimer, de novo protein; 1.90A {Synthetic} SCOP: h.1.3.1 PDB: 1kdd_A 1kd9_A

Probab=80.07  E-value=3.5  Score=24.92  Aligned_cols=27  Identities=19%  Similarity=0.412  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKA   49 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~   49 (136)
                      ++||-.++++|-.++..|+.+...|+.
T Consensus         3 MnQLE~kVEeLl~~~~~Le~EV~RL~~   29 (36)
T 1kd8_A            3 VKQLEAEVEEIESEVWHLENEVARLEK   29 (36)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            355666666665555555555555543

>2ve7_C Kinetochore protein NUF2, kinetochore protein SPC; mitosis, centromere, cell cycle, microtubule, C division, calponin homology; 2.88A {Homo sapiens} PDB: 3iz0_D*

Probab=80.06  E-value=1.6  Score=35.11  Aligned_cols=31  Identities=23%  Similarity=0.289  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 032660           43 KIKELKAEKNELRDEKQRLKADKEKLEQQVK   73 (136)
Q Consensus        43 e~~~L~~EKnELrdEk~~Lk~eke~Le~qlk   73 (136)
                      +.++++.+.+.|++|++.+++++++|+.++.
T Consensus       149 ~~e~~~~~i~ql~~En~~le~~Ie~Lk~e~~  179 (250)
T 2ve7_C          149 QYKSSADKMQQLNAAHQEALMKLERLEKEVD  179 (250)
T ss_dssp             HTTHHHHHHHHHHHHHHHHHHSCC-------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3333333333344444444444444444433

---

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	136
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	6e-09
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	7e-07
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	3e-06
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	8e-06
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	5e-05
d1a5za2	172	d.162.1.1 (A:164-333) Lactate dehydrogenase {Therm	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 = 47.6 bits (113), Expect = 6e-09
 Identities = 10/55 (18%), Positives = 23/55 (41%)

Query: 1  MLEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR 55
           +   +  K  +A IL      ++ +R +    +Q  +DL+ +   L+ +   L 
Sbjct: 27 SVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRALG 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 = 42.2 bits (99), Expect = 7e-07
 Identities = 12/51 (23%), Positives = 23/51 (45%)

Query: 5  GRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELR 55
              K  K  IL      +  ++ E QKL    + L+++ ++LK +  +L 
Sbjct: 36 ENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQLG 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 = 40.3 bits (94), Expect = 3e-06
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 2  LEPGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEK 51
          L  G   K +K+ +L   +  +  L+   QKLKQ    L+  + + K+ K
Sbjct: 31 LVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSKSLK 80

>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 = 38.9 bits (91), Expect = 8e-06
 Identities = 10/45 (22%), Positives = 20/45 (44%)

Query: 4  PGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELK 48
           G   K  K+ +L   +  ++ L+    KL+Q    L+   ++ K
Sbjct: 16 MGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQKNK 60

>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 = 37.2 bits (86), Expect = 5e-05
 Identities = 7/48 (14%), Positives = 20/48 (41%)

Query: 6  RPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNE 53
             +    ++L+     +++L    +K     + LQ + + LK +  +
Sbjct: 32 DSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLEK 79

>d1a5za2 d.162.1.1 (A:164-333) Lactate dehydrogenase {Thermotoga maritima [TaxId: 2336]} Length = 172

class: Alpha and beta proteins (a+b)
fold: LDH C-terminal domain-like
superfamily: LDH C-terminal domain-like
family: Lactate & malate dehydrogenases, C-terminal domain
domain: Lactate dehydrogenase
species: Thermotoga maritima [TaxId: 2336]

 Score = 33.7 bits (76), Expect = 0.003
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 29  EAQKLKQSTEDLQEKIKELKAEKN 52
           E +  ++S   L+  I E+ AE+N
Sbjct: 149 ELEAFRKSASILKNAINEITAEEN 172

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	136
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	98.84
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	98.56
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	98.37
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	98.36
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	98.33
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	96.52
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	95.83
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	95.2
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	93.75
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	88.42
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	88.11
d1fxkc_	133	Prefoldin alpha subunit {Archaeon Methanobacterium	86.97
d1ivsa1	66	Valyl-tRNA synthetase (ValRS) C-terminal domain {T	85.88
d2p90a1	269	Hypothetical protein Cgl1923 {Corynebacterium glut	84.94
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	82.68

>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=98.84  E-value=2.8e-09  Score=68.45  Aligned_cols=42  Identities=21%  Similarity=0.286  Sum_probs=37.2

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Q 032660            4 PGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIK   45 (136)
Q Consensus         4 P~rp~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~   45 (136)
                      |+-.+|+|||+||.+||.||++|+.+++.|++++..|+.+.+
T Consensus        16 P~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~~   57 (61)
T d1uklc_          16 MGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQ   57 (61)
T ss_dssp             SCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            554479999999999999999999999999999998887654

>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=98.56  E-value=9e-08  Score=63.64  Aligned_cols=45  Identities=27%  Similarity=0.402  Sum_probs=39.8

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Q 032660            4 PGRPPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELK   48 (136)
Q Consensus         4 P~rp~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~   48 (136)
                      |+...|+||++||.+||.||++|..+.+.|++++..|+.+++.++
T Consensus        33 P~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~~~~~~   77 (80)
T d1am9a_          33 VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (80)
T ss_dssp             TCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            666679999999999999999999999999999888887776654

>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=98.37  E-value=2.6e-07  Score=61.38  Aligned_cols=47  Identities=19%  Similarity=0.320  Sum_probs=36.4

Q ss_pred             CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 032660            7 PPKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNE   53 (136)
Q Consensus         7 p~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnE   53 (136)
                      ..|++|++||..||.||++|+.+.++|..+++.|..+...|..+.++
T Consensus        33 ~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~   79 (83)
T d1nkpb_          33 GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRA   79 (83)
T ss_dssp             TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36899999999999999999998888887766666555555544443

>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=98.36  E-value=4.9e-07  Score=60.59  Aligned_cols=47  Identities=26%  Similarity=0.356  Sum_probs=39.1

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNEL   54 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnEL   54 (136)
                      .|.+|++||..||.||++|+.++++|..+.+.|..+...|..+.+.|
T Consensus        39 ~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~L   85 (88)
T d1nkpa_          39 EKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQL   85 (88)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999999988887777776666666666555

>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=98.33  E-value=6.6e-07  Score=58.87  Aligned_cols=43  Identities=16%  Similarity=0.315  Sum_probs=37.4

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQKLKQSTEDLQEKIKELKAE   50 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~~Lk~~n~~L~ee~~~L~~E   50 (136)
                      .|++|++||.+||.||++|+.+++.|..++..|..+.+.|..+
T Consensus        34 ~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~~~~~L~~~   76 (79)
T d1nlwa_          34 SRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQ   76 (79)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999998888888777777777654

>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=96.52  E-value=0.00044  Score=43.46  Aligned_cols=26  Identities=19%  Similarity=0.311  Sum_probs=22.3

Q ss_pred             CCCCCCchhhhHHHHHHHHHHHHHHH
Q 032660            5 GRPPKTDKATILSDVVRMMEQLRTEA   30 (136)
Q Consensus         5 ~rp~K~DKAsIL~DAir~lkqLr~e~   30 (136)
                      +...|+|||+||.+||.||++|+.++
T Consensus        36 ~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_          36 NVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             SCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             CCcccccHHHHHHHHHHHHHHHHHhh
Confidence            34469999999999999999998754

>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=95.83  E-value=0.0024  Score=40.72  Aligned_cols=24  Identities=25%  Similarity=0.419  Sum_probs=21.3

Q ss_pred             CCCchhhhHHHHHHHHHHHHHHHH
Q 032660            8 PKTDKATILSDVVRMMEQLRTEAQ   31 (136)
Q Consensus         8 ~K~DKAsIL~DAir~lkqLr~e~~   31 (136)
                      .|.||++||..||.||++|+..++
T Consensus        44 ~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          44 QRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHhh
Confidence            489999999999999999987653

>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=95.20  E-value=0.0022  Score=40.37  Aligned_cols=26  Identities=23%  Similarity=0.332  Sum_probs=22.2

Q ss_pred             CCCCCCchhhhHHHHHHHHHHHHHHH
Q 032660            5 GRPPKTDKATILSDVVRMMEQLRTEA   30 (136)
Q Consensus         5 ~rp~K~DKAsIL~DAir~lkqLr~e~   30 (136)
                      ++..|.+|++||..|+.||++|+.+-
T Consensus        38 ~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_          38 STKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             SSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            34569999999999999999998653

>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=93.75  E-value=0.5  Score=31.18  Aligned_cols=55  Identities=20%  Similarity=0.410  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHH--------HHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           21 RMMEQLRTEAQKLKQSTEDLQEKI--------KELKAEKNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        21 r~lkqLr~e~~~Lk~~n~~L~ee~--------~~L~~EKnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      .-.++|+.+++.|+++...+..++        .+|..|-++|.++...|+.+...++.++..+
T Consensus        35 ~~rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~~~l~~~   97 (110)
T d1seta1          35 REVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEAL   97 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344566666777777666666555        3344444444444444444444444555543

>d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Seryl-tRNA synthetase (SerRS)
domain: Seryl-tRNA synthetase (SerRS)
species: Thermus thermophilus, strain hb27 [TaxId: 274]

Probab=88.42  E-value=2  Score=28.01  Aligned_cols=54  Identities=20%  Similarity=0.346  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHH--------HHHHHHHHHHhHHHHHHHHHHHHhc
Q 032660           22 MMEQLRTEAQKLKQSTEDLQEKIKELKAE--------KNELRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~ee~~~L~~E--------KnELrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      -|-.|-.+-.+|..+.+.|+.+.+.+..+        +.+|.++-..|+.++..|+.+++.+
T Consensus        29 ~i~~ld~~rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~   90 (110)
T d1seta1          29 ALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREK   90 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455556666666666666666655432        3455666667777777777777764

>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=88.11  E-value=0.91  Score=28.87  Aligned_cols=20  Identities=5%  Similarity=0.164  Sum_probs=8.6

Q ss_pred             HHHHHHHHHHHHHHhhHHHH
Q 032660           22 MMEQLRTEAQKLKQSTEDLQ   41 (136)
Q Consensus        22 ~lkqLr~e~~~Lk~~n~~L~   41 (136)
                      +|+.-..-|+.|++.+..|.
T Consensus        46 iL~~A~~yI~~L~~~~~~l~   65 (88)
T d1nkpa_          46 ILKKATAYILSVQAEEQKLI   65 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            44444444444444443333

>d1fxkc_ a.2.5.1 (C:) Prefoldin alpha subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Prefoldin
family: Prefoldin
domain: Prefoldin alpha subunit
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=86.97  E-value=1  Score=30.04  Aligned_cols=40  Identities=15%  Similarity=0.272  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhH
Q 032660           23 MEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLK   62 (136)
Q Consensus        23 lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk   62 (136)
                      |.+|..+++.|+.....|++++..|....+|+..-+..|+
T Consensus         3 L~eL~~~~~~l~~~l~~l~~~i~~l~~~~~e~~~~~~~L~   42 (133)
T d1fxkc_           3 LAEIVAQLNIYQSQVELIQQQMEAVRATISELEILEKTLS   42 (133)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566666666666666666666666666655554444443

>d1ivsa1 a.2.7.3 (A:797-862) Valyl-tRNA synthetase (ValRS) C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Valyl-tRNA synthetase (ValRS) C-terminal domain
domain: Valyl-tRNA synthetase (ValRS) C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=85.88  E-value=2.1  Score=25.93  Aligned_cols=22  Identities=5%  Similarity=0.125  Sum_probs=15.1

Q ss_pred             HHHHHHHhHHHHHHHHHHHHhc
Q 032660           54 LRDEKQRLKADKEKLEQQVKAM   75 (136)
Q Consensus        54 LrdEk~~Lk~eke~Le~qlk~~   75 (136)
                      -|+....+..++++|+.+|..|
T Consensus        44 ~k~kl~~~~~~~~~l~~~l~~L   65 (66)
T d1ivsa1          44 EEARLKENLEQAERIREALSQI   65 (66)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhh
Confidence            3455566777888888877664

>d2p90a1 c.56.8.1 (A:6-274) Hypothetical protein Cgl1923 {Corynebacterium glutamicum [TaxId: 1718]}

class: Alpha and beta proteins (a/b)
fold: Phosphorylase/hydrolase-like
superfamily: Cgl1923-like
family: Cgl1923-like
domain: Hypothetical protein Cgl1923
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=84.94  E-value=0.66  Score=34.65  Aligned_cols=55  Identities=15%  Similarity=0.282  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           19 VVRMMEQLRTEAQKLKQSTEDLQEKIKELKAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        19 Air~lkqLr~e~~~Lk~~n~~L~ee~~~L~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      |..+|+-| +++=.|+-....|.++.+....+.++|.++...++.=.++||+|+-+
T Consensus       209 A~~lL~~l-~~~~gl~id~~~L~e~Ae~~e~~i~~l~e~~~e~~~~v~~LE~~yD~  263 (269)
T d2p90a1         209 TLKLLQSI-ADSADLNLPLLALERDAEKVHRQLMEQTEESSEIQRVVGALEQQYDS  263 (269)
T ss_dssp             HHHHHHHH-HHHHTCCCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHCCCCChHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhHhh
Confidence            34445544 44456777888888888888899999999999999999999999865

>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=82.68  E-value=2.1  Score=26.76  Aligned_cols=27  Identities=30%  Similarity=0.428  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 032660           48 KAEKNELRDEKQRLKADKEKLEQQVKA   74 (136)
Q Consensus        48 ~~EKnELrdEk~~Lk~eke~Le~qlk~   74 (136)
                      ..+..+|.+++..|+.+.+.|++++..
T Consensus        53 ~~~~~~l~~~~~~l~~~~~~L~~~l~~   79 (83)
T d1nkpb_          53 RRKNHTHQQDIDDLKRQNALLEQQVRA   79 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444445555443