Citrus Sinensis ID: 022306

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------30
Protein Sequence
MSIATSTKTSSRSSLLSSPSLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKNANSNQDSDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEAREAYITAVAMAKEKQDEESMATAARARLHLQSFVFRNSRRES
Secondary Structure (PSIPRED)
ccccccccccccccccccHHHHHcccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccEEccccccccccccccccHHHccccccccEEEEEEEcccccHHHHcccccccccccccccccccHcccccccccccccccccccccccccccHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
msiatstktssrssllsspslydrkasssftrrgsmiytktpsresllkkttdpkgrnaaqslppkrkkdngdkdlgknansnqdsdsfsIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLikndstvnadddydikpyysdylsdiddldDVEMQRMEEAREAYITAVAMAKEKQDEESMATAARARLHLQSFVFRNSRRES
Flexible Loop (DISEMBL)
msiatstktssrssllsspslydrkasssftrrgsmiytktpsresllkkttdpkgrnaaqslppkrkkdngdkdlgknansnqdsdsfsIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLkslessksqvNAVHLKLDELKRLAAEKDSlikstqlqlsdAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEAREAYITAVAMAKEKQDEESMATAARARLhlqsfvfrnsrres
Low Complexity Region (SEG)
MsiatstktssrssllsspslYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPkrkkdngdkdlgknanSNQDSDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFekdellkslessksQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPyysdylsdiddlddVEMQRMEEAREAYITAVAMAKEKQDEESMATAARARLHLQSFVFRNSRRES
Disordered region (IsUnstruct)
*****************************************************************************************************************************************************************************************************************FMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDV**********AYITAV**********************************
Disordered Region (DISOPRED)
********************************************************************************************************************************************************************************************************************************************************************YITAVAM******EE*MATAARARLHLQSFV*RN*****
Disordered Region (DISEMBL)
****************************SFTRRGSMIYTKTPSRESLLKK*********************GDKDLGKNANSNQDSDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLAD*******************************EMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEAREAYITAVAM************AARARLHLQSFVFRNSRRES
Disordered Region (DISPRO)
****************************SFTRRGSMIYTKTP*********************************************************EKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEAREAYITAVAMAKEKQDEESMATAARARLHLQSFVFRN*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSIATSTKTSSRSSLLSSPSLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKNANSNQDSDSFSIFSSRALVxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAAxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVExxxxxxxxxxxxxxxxxxxxxQDEESMATAARARLHLQSFVFRNSRRES
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

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	299
224077546	340	predicted protein [Populus trichocarpa]	0.909	0.8	0.718	1e-104
255547095	367	conserved hypothetical protein [Ricinus	0.929	0.757	0.732	5e-99
225455714	368	PREDICTED: uncharacterized protein LOC10	0.916	0.744	0.693	1e-95
356562648	327	PREDICTED: uncharacterized protein LOC10	0.906	0.828	0.631	5e-91
356511562	327	PREDICTED: uncharacterized protein LOC10	0.906	0.828	0.635	1e-90
449439357	350	PREDICTED: uncharacterized protein LOC10	0.909	0.777	0.631	6e-72
449486894	350	PREDICTED: uncharacterized protein LOC10	0.909	0.777	0.635	9e-70
365222918	336	Hop-interacting protein THI110 [Solanum	0.889	0.791	0.576	4e-69
83265567	338	microtubule-associated protein [Nicotian	0.896	0.792	0.547	9e-67
297810915	325	hypothetical protein ARALYDRAFT_487645 [	0.859	0.790	0.525	1e-65

>gi|224077546|ref|XP_002305296.1| predicted protein [Populus trichocarpa] gi|222848260|gb|EEE85807.1| predicted protein [Populus trichocarpa]

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 197/274 (71%), Positives = 228/274 (83%), Gaps = 2/274 (0%)

Query: 20  SLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKN 79
           SL DRK S+SFTRRGS+IYTKTPSRESL KK  DP+GRN  QS+P K+K D+GDKD GK 
Sbjct: 68  SLIDRKVSTSFTRRGSVIYTKTPSRESLSKKMIDPRGRNTCQSIPTKKKMDHGDKDQGKT 127

Query: 80  ANSNQDSDSFSIFSS-RALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVN 138
           AN NQD+DSF+I SS RA+ + K+ EEL+ALREQVEDLQRK+ EKDELLKS E SK+Q+N
Sbjct: 128 ANDNQDADSFAILSSSRAVPTGKDAEELIALREQVEDLQRKLLEKDELLKSAEVSKNQMN 187

Query: 139 AVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQE 198
           AVH + DE+K   AEKDSLIKSTQLQLS+AKIKLADKQAALEK QWEAMT ++K E LQ+
Sbjct: 188 AVHAEFDEVKLQVAEKDSLIKSTQLQLSNAKIKLADKQAALEKLQWEAMTSNQKVETLQQ 247

Query: 199 EVESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEAR 258
           E++S+QG +SSFM +FE L KN+S   A +DYDIKP Y D L DIDDLDD EMQ+MEEAR
Sbjct: 248 ELDSIQGGISSFMLVFENLTKNNSIPYA-EDYDIKPCYLDQLPDIDDLDDREMQKMEEAR 306

Query: 259 EAYITAVAMAKEKQDEESMATAARARLHLQSFVF 292
           EAYI AVA AKEKQDE+S+A AA ARLHLQSFVF
Sbjct: 307 EAYIAAVASAKEKQDEKSIAAAASARLHLQSFVF 340

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255547095|ref|XP_002514605.1| conserved hypothetical protein [Ricinus communis] gi|223546209|gb|EEF47711.1| conserved hypothetical protein [Ricinus communis]

 Score =  367 bits (941), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 205/280 (73%), Positives = 237/280 (84%), Gaps = 2/280 (0%)

Query: 20  SLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKN 79
           SL  RK +SSFTRRGSMIYTKTPSR+SL KK TDPKGRNA+QS+P K+KK++GDKD GK+
Sbjct: 72  SLIHRKGNSSFTRRGSMIYTKTPSRDSLYKKMTDPKGRNASQSIPTKKKKEHGDKDRGKS 131

Query: 80  ANSNQDSDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNA 139
             +NQDSD+FSIFSSR+L SEK+IEELV LREQVEDLQRK+ EKDELLKS E SK+Q+N 
Sbjct: 132 GGNNQDSDNFSIFSSRSLASEKDIEELVTLREQVEDLQRKLAEKDELLKSAEISKNQMND 191

Query: 140 VHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEE 199
           VH KLDELK  AAEKDSLIKS QLQLSDAKIKLADKQAALEK +WEAMT + K EKLQEE
Sbjct: 192 VHGKLDELKHQAAEKDSLIKSIQLQLSDAKIKLADKQAALEKIRWEAMTSNTKVEKLQEE 251

Query: 200 VESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEARE 259
           ++S QG++SS M +FEGL  N+ST  A +DYD+ P Y DYL DIDD+DD+EMQ MEEAR+
Sbjct: 252 LDSKQGDISSMMLLFEGLT-NESTKIA-EDYDVNPRYLDYLPDIDDMDDIEMQEMEEARQ 309

Query: 260 AYITAVAMAKEKQDEESMATAARARLHLQSFVFRNSRRES 299
           AYI AVA AKEKQDEES+A AA ARLHLQSFV R++ R +
Sbjct: 310 AYIAAVATAKEKQDEESIAAAASARLHLQSFVLRSNGRNA 349

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225455714|ref|XP_002273093.1| PREDICTED: uncharacterized protein LOC100247402 [Vitis vinifera] gi|297734104|emb|CBI15351.3| unnamed protein product [Vitis vinifera]

 Score =  355 bits (912), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 192/277 (69%), Positives = 235/277 (84%), Gaps = 3/277 (1%)

Query: 20  SLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKN 79
           SL DRKASSSFTR G++ YTKTPSRESL ++ ++ KGRN AQS+P K+++D+G+KD G+N
Sbjct: 69  SLIDRKASSSFTRVGAVTYTKTPSRESLSRRFSELKGRNTAQSIPTKKRRDHGEKDQGRN 128

Query: 80  ANSNQD--SDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQV 137
            ++NQD  +D FS+FSSRA+ SEK+ EEL+ALREQVEDLQRK+ EKDELLKS E SKSQ+
Sbjct: 129 GSNNQDGCADGFSLFSSRAVASEKDKEELIALREQVEDLQRKLAEKDELLKSAEISKSQM 188

Query: 138 NAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQ 197
           +AVH KLDELK+  AEKDSLIKSTQLQLSDAKIKLADKQAALEK QWEAMT +RK EKLQ
Sbjct: 189 SAVHDKLDELKQQVAEKDSLIKSTQLQLSDAKIKLADKQAALEKIQWEAMTSNRKVEKLQ 248

Query: 198 EEVESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEA 257
           E++ESMQ ++SSFM +FEGL KNDST+ + + YDI PY+  +L  IDDLD++  Q+MEEA
Sbjct: 249 EDLESMQADISSFMLLFEGLTKNDSTIRS-ESYDITPYHLGHLPPIDDLDEIGAQKMEEA 307

Query: 258 REAYITAVAMAKEKQDEESMATAARARLHLQSFVFRN 294
           R+AY+ AVA AKE QDEES+A AA +RLHLQSFVF+N
Sbjct: 308 RKAYVAAVAAAKENQDEESIALAANSRLHLQSFVFKN 344

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562648|ref|XP_003549581.1| PREDICTED: uncharacterized protein LOC100806411 [Glycine max]

 Score =  340 bits (871), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 173/274 (63%), Positives = 223/274 (81%), Gaps = 3/274 (1%)

Query: 20  SLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKN 79
           SL DRKAS SFTRRGSMIYTKTP+RESL K+ TD K RN A S+P K+K+D+G+K+ GKN
Sbjct: 51  SLIDRKASRSFTRRGSMIYTKTPTRESLSKRVTDSKSRNVAPSIPAKKKRDHGEKEQGKN 110

Query: 80  ANSNQDSDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNA 139
            ++  D+D++S+FSSR L SEK+IEEL  L+EQVE+LQRK+ EKDELLKS E+++ Q+N 
Sbjct: 111 GSN--DADNYSMFSSRTLASEKDIEELGMLKEQVEELQRKLLEKDELLKSAENTRDQMNV 168

Query: 140 VHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEE 199
            + KLDELK  A+EK+SL+K TQ QLSDAKIKLADKQAALEK QWEAMT ++K +KLQ+E
Sbjct: 169 FNAKLDELKHQASEKESLLKYTQQQLSDAKIKLADKQAALEKIQWEAMTSNKKVDKLQDE 228

Query: 200 VESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEARE 259
           + SMQ +++SF  + EGL K D T    DDYD+KPY   +L  IDDLD++E+Q+MEEAR+
Sbjct: 229 LGSMQADITSFTLLLEGLSKTD-TAKYTDDYDVKPYDFSHLPSIDDLDEMELQKMEEARK 287

Query: 260 AYITAVAMAKEKQDEESMATAARARLHLQSFVFR 293
           +Y+ AV+++KEK+DEES+A AA ARLHLQS VF+
Sbjct: 288 SYMAAVSVSKEKRDEESIAAAANARLHLQSLVFK 321

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356511562|ref|XP_003524494.1| PREDICTED: uncharacterized protein LOC100799930 [Glycine max]

 Score =  338 bits (868), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 174/274 (63%), Positives = 224/274 (81%), Gaps = 3/274 (1%)

Query: 20  SLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKN 79
           SL DRKAS SFTRRGSMIYTKTP+RESL K+TTD K RN AQS+  K+K+D+G+K+ GKN
Sbjct: 51  SLIDRKASRSFTRRGSMIYTKTPTRESLSKRTTDSKSRNVAQSILAKKKRDHGEKEQGKN 110

Query: 80  ANSNQDSDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNA 139
            ++  D+D++S+FS+R L SEK+IEEL  L+EQVE+LQRK+ EKDELLKS E+S+ Q+NA
Sbjct: 111 GSN--DADNYSMFSTRTLASEKDIEELGMLKEQVEELQRKLLEKDELLKSAENSRDQMNA 168

Query: 140 VHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEE 199
            + KLDELK  A+EK+SL+K TQ QLSDAKIKLADKQAALEK QWEAMT ++K +KL +E
Sbjct: 169 FNAKLDELKHQASEKESLLKYTQQQLSDAKIKLADKQAALEKIQWEAMTSNKKVDKLLDE 228

Query: 200 VESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEARE 259
           + SMQ +++SF  + EGL K D T    +DYD+KPY   +L  IDDLD+VE+Q+M+EAR+
Sbjct: 229 LGSMQADITSFTLLLEGLSKTD-TAKYTNDYDVKPYDFSHLPSIDDLDEVELQKMDEARK 287

Query: 260 AYITAVAMAKEKQDEESMATAARARLHLQSFVFR 293
           AY+ AV+++KEK+DEES+A AA ARLHLQS VF+
Sbjct: 288 AYMAAVSISKEKRDEESIAAAANARLHLQSLVFK 321

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439357|ref|XP_004137452.1| PREDICTED: uncharacterized protein LOC101207962 [Cucumis sativus]

 Score =  276 bits (707), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 173/274 (63%), Positives = 215/274 (78%), Gaps = 2/274 (0%)

Query: 20  SLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKN 79
           SL DRKASSSFT+RGSMIYTKTPSR+SL +K  + KG+N  QS+P K+KKD+GDK+ G N
Sbjct: 78  SLIDRKASSSFTKRGSMIYTKTPSRDSLHRKI-EQKGKNNGQSIPTKKKKDHGDKEEGHN 136

Query: 80  ANSNQDSDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNA 139
            ++N D++ FS+FSS +LVSEKE EEL+ LREQVEDLQ+K+ EK+ELLKS E SK Q+N 
Sbjct: 137 VDNNGDANGFSMFSSSSLVSEKEKEELITLREQVEDLQKKLLEKEELLKSAEMSKDQMNN 196

Query: 140 VHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEE 199
           V+ KLD L   +AEKDS+IKS   QLSDAKIKLADKQAALEK QWE  T + K E+LQE+
Sbjct: 197 VYSKLDALSLQSAEKDSMIKSIHSQLSDAKIKLADKQAALEKIQWEVTTSNTKVEELQEQ 256

Query: 200 VESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEARE 259
           ++S QG++SSFM + EGL K D + +   DY++  +  +    IDDLDDVEM++MEEAR+
Sbjct: 257 LKSSQGDVSSFMLLLEGLTKKDCS-DRLKDYNLSLHLPESCPSIDDLDDVEMKKMEEARQ 315

Query: 260 AYITAVAMAKEKQDEESMATAARARLHLQSFVFR 293
           AY+  VA AK KQDEES+A AA ARLHLQSFVFR
Sbjct: 316 AYVAVVAAAKAKQDEESIAAAATARLHLQSFVFR 349

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449486894|ref|XP_004157434.1| PREDICTED: uncharacterized protein LOC101224915 [Cucumis sativus]

 Score =  269 bits (688), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 174/274 (63%), Positives = 216/274 (78%), Gaps = 2/274 (0%)

Query: 20  SLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKN 79
           SL DRKASSSFT+RGSMIYTKTPSR+SL +K  + KG+N  QS+P K+KKD+GDK+ G N
Sbjct: 78  SLIDRKASSSFTKRGSMIYTKTPSRDSLHRKI-EQKGKNNGQSIPTKKKKDHGDKEEGHN 136

Query: 80  ANSNQDSDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNA 139
            ++N D++ FS+FSS +LVSEKE EEL+ LREQVEDLQ+K+ EK+ELLKS E SK Q+N 
Sbjct: 137 VDNNGDANGFSMFSSSSLVSEKEKEELITLREQVEDLQKKLLEKEELLKSAEMSKDQMNN 196

Query: 140 VHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEE 199
           V+ KLD L   +AEKDS+IKS   QLSDAKIKLADKQAALEK QWE  T + K E+LQE+
Sbjct: 197 VYSKLDALSLQSAEKDSMIKSIHSQLSDAKIKLADKQAALEKIQWEVTTSNTKVEELQEQ 256

Query: 200 VESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEARE 259
           ++S QG++SSFM + EGL K D + +   DY++  +  +    IDDLDDVEM++MEEAR+
Sbjct: 257 LKSSQGDVSSFMLLLEGLTKKDCS-DRLKDYNLSLHLPESCPSIDDLDDVEMKKMEEARQ 315

Query: 260 AYITAVAMAKEKQDEESMATAARARLHLQSFVFR 293
           AY+ AVA AK KQDEES+A AA ARLHLQSFVFR
Sbjct: 316 AYVAAVAAAKAKQDEESIAAAATARLHLQSFVFR 349

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|365222918|gb|AEW69811.1| Hop-interacting protein THI110 [Solanum lycopersicum]

 Score =  267 bits (682), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 159/276 (57%), Positives = 206/276 (74%), Gaps = 10/276 (3%)

Query: 20  SLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKN 79
           SL DRKA SSFTRRGSM YTKTPSRESL KKT++ KG+NAAQS    R       D  KN
Sbjct: 68  SLIDRKAKSSFTRRGSMTYTKTPSRESLYKKTSETKGKNAAQSNKKHR-------DQNKN 120

Query: 80  ANSNQD--SDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQV 137
             ++QD  SD+ S+ SSR+ +SEK+ EEL+ALR QVEDLQ+K+ EKDELLK +E SK+++
Sbjct: 121 VGADQDGCSDNISMPSSRSYLSEKDREELMALRGQVEDLQKKLSEKDELLKEVEISKNEM 180

Query: 138 NAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQ 197
            +++ KLDE+K+  AEK+SL+K TQ+QLSDAK+KLADKQAA+EK +WEA T S+K EKLQ
Sbjct: 181 ASIYAKLDEMKKEYAEKESLLKLTQVQLSDAKVKLADKQAAVEKLEWEATTSSKKVEKLQ 240

Query: 198 EEVESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEA 257
           E++E ++ E++ FMQ  + L KNDS   A +DYD+ PY  D   + D  +++ M+ +E A
Sbjct: 241 EDLEVVRQEIAWFMQFVQQLTKNDSRTLA-EDYDVIPYLCDKNIETDQPNELGMEEVELA 299

Query: 258 REAYITAVAMAKEKQDEESMATAARARLHLQSFVFR 293
           REAYI AVA AKE QDE S + AA+ARL+LQS V R
Sbjct: 300 REAYIAAVAAAKENQDEASFSEAAKARLYLQSLVLR 335

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|83265567|gb|ABB97536.1| microtubule-associated protein [Nicotiana benthamiana]

 Score =  259 bits (663), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 151/276 (54%), Positives = 200/276 (72%), Gaps = 8/276 (2%)

Query: 20  SLYDRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKN 79
           SL DRK  SSF+RRGSM YTKTP +ESL KKT++ KGRNAAQS   K+ +        KN
Sbjct: 68  SLIDRKTKSSFSRRGSMTYTKTPPKESLYKKTSEAKGRNAAQSTATKKHRGQN-----KN 122

Query: 80  ANSNQD--SDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQV 137
             SNQD  +++FS+ SSR+ + EK+ EEL+ALREQVEDL +K+ EKDELLK +E +K+++
Sbjct: 123 VGSNQDGCTENFSMISSRSPLLEKDREELMALREQVEDLHKKLSEKDELLKEVEIAKNEM 182

Query: 138 NAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQ 197
            ++  KLDE+K+  AEKDSL+KSTQ+QLSDAK+ LADKQAA+EK +WEAMT S+K +KLQ
Sbjct: 183 ASICAKLDEMKKEYAEKDSLLKSTQVQLSDAKVILADKQAAVEKLEWEAMTSSKKVDKLQ 242

Query: 198 EEVESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEA 257
            +++ ++ E++ FMQ  + L KN S   A +DYD  PY  D   + D  +   MQ +E A
Sbjct: 243 NDLDVVRQEIAWFMQFVQKLTKNGSRALA-EDYDAIPYLCDKNLETDHPNKTGMQELEMA 301

Query: 258 REAYITAVAMAKEKQDEESMATAARARLHLQSFVFR 293
           REAY+ A+A AKE QDE S + AA+ARL+LQS V R
Sbjct: 302 REAYLAAIAAAKENQDEASFSAAAKARLYLQSLVLR 337

Source: Nicotiana benthamiana

Species: Nicotiana benthamiana

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297810915|ref|XP_002873341.1| hypothetical protein ARALYDRAFT_487645 [Arabidopsis lyrata subsp. lyrata] gi|297319178|gb|EFH49600.1| hypothetical protein ARALYDRAFT_487645 [Arabidopsis lyrata subsp. lyrata]

 Score =  256 bits (653), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 142/270 (52%), Positives = 191/270 (70%), Gaps = 13/270 (4%)

Query: 23  DRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPKRKKDNGDKDLGKNANS 82
           + K  SSF RRGSMIYTK PS+ESL ++     GRNA+Q+ P ++K+D    D   N NS
Sbjct: 68  EHKERSSFKRRGSMIYTKMPSKESLSRR-----GRNASQTAPGRKKRDQEGNDDVMN-NS 121

Query: 83  NQDSDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHL 142
            +D ++ +  S        E EEL  LREQV DLQ K+FEK+E+LKS+E SK+QVN +  
Sbjct: 122 REDGENATALSG------AEKEELSRLREQVNDLQTKLFEKEEVLKSMEMSKNQVNDIQE 175

Query: 143 KLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVES 202
           KL+   RL AEK+ LIKS QLQLSD KIKLADKQAALEK+QWEA T   +A KLQE++++
Sbjct: 176 KLEATNRLVAEKEMLIKSMQLQLSDTKIKLADKQAALEKTQWEAKTTGTRAIKLQEQLDA 235

Query: 203 MQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEAREAYI 262
           +QG++S+F ++FE L K DS    D DYD  PY  D+L  +DD+D+ +++++EEAR AY+
Sbjct: 236 VQGDISTFTRVFETLAKTDSK-KPDRDYDATPYEFDHLPYLDDVDETDLRKIEEARLAYV 294

Query: 263 TAVAMAKEKQDEESMATAARARLHLQSFVF 292
            AV  AKE+++EES+A AA+AR +LQS  F
Sbjct: 295 AAVTTAKERENEESLAMAAQARAYLQSLAF 324

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	299
TAIR|locus:2181534	326	MPB2C "movement protein bindin	0.859	0.788	0.448	2e-49

TAIR|locus:2181534 MPB2C "movement protein binding protein 2C" [Arabidopsis thaliana (taxid:3702)]

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 121/270 (44%), Positives = 162/270 (60%)

Query:    23 DRKASSSFTRRGSMIYTKTPSRESLLKKTTDPKGRNAAQSLPPXXXXXXXXXXXXXXXXS 82
             + K  SSF RRGSMIYTK PS+ESL ++     GRNA+Q++P                 S
Sbjct:    68 EHKERSSFKRRGSMIYTKMPSKESLSRR-----GRNASQTVP-GRKKRDQEGNDDVMNNS 121

Query:    83 NQDSDSFSIFSSRALVSEKEIEELVALREQVEDLQRKMFXXXXXXXXXXXXXXQVNAVHL 142
              +D ++     ++AL   ++ EE+  LREQV DLQ K+               QVN +  
Sbjct:   122 REDDEN-----AKALAGAEK-EEMSRLREQVNDLQTKLSEKEEVLKSMEMSKNQVNEIQE 175

Query:   143 KLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVES 202
             KL+   RL AEKD LIKS QLQLSD KIKLADKQAALEK+QWEA T   +A KLQE++++
Sbjct:   176 KLEATNRLVAEKDMLIKSMQLQLSDTKIKLADKQAALEKTQWEAKTTGTRAIKLQEQLDA 235

Query:   203 MQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPXXXXXXXXXXXXXXVEMQRMEEAREAYI 262
             ++G++S+F ++FE L K DS    D DYD  P               ++++MEEAR AY+
Sbjct:   236 VEGDISTFTRVFETLAKTDSK-KPDRDYDAVPYEFDHLPYLDDVDETDLRKMEEARLAYV 294

Query:   263 TAVAMAKEKQDEESMATAARARLHLQSFVF 292
              AV  AKE++DEES+  AA+AR +LQS  F
Sbjct:   295 AAVNTAKEREDEESLVMAAQARAYLQSLAF 324


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.310   0.122   0.312    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      299       235   0.00088  113 3  10 23  0.47    33
                                                     32  0.43    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  594 (63 KB)
  Total size of DFA:  205 KB (2116 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  35.87u 0.10s 35.97t   Elapsed:  00:00:02
  Total cpu time:  35.87u 0.10s 35.97t   Elapsed:  00:00:02
  Start:  Thu May  9 15:10:32 2013   End:  Thu May  9 15:10:34 2013

GO:0005634 "nucleus" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0015630 "microtubule cytoskeleton" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IMP

GO:0010375 "stomatal complex patterning" evidence=IMP

GO:0010497 "plasmodesmata-mediated intercellular transport" evidence=IMP

GO:0043622 "cortical microtubule organization" evidence=IMP

GO:0051607 "defense response to virus" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.IV.4200.1 hypothetical protein (340 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	299
PRK11637	428	AmiB activator; Provisional	96.76
PF10186	302	Atg14: UV radiation resistance protein and autopha	96.39
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	95.94
PRK09039	343	hypothetical protein; Validated	95.92
PRK11637	428	AmiB activator; Provisional	95.8
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	95.77
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	95.63
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	95.28
PRK09039	343	hypothetical protein; Validated	95.26
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	95.13
PHA02562	562	46 endonuclease subunit; Provisional	95.03
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	94.83
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	94.73
cd07664	234	BAR_SNX2 The Bin/Amphiphysin/Rvs (BAR) domain of S	94.67
PF00038	312	Filament: Intermediate filament protein; InterPro:	94.63
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	94.59
PRK03918	880	chromosome segregation protein; Provisional	94.57
PRK03918	880	chromosome segregation protein; Provisional	94.51
KOG0996	1293	consensus Structural maintenance of chromosome pro	94.46
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	94.36
KOG0243	1041	consensus Kinesin-like protein [Cytoskeleton]	94.35
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	94.2
cd07665	234	BAR_SNX1 The Bin/Amphiphysin/Rvs (BAR) domain of S	94.17
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	94.16
PHA02562	562	46 endonuclease subunit; Provisional	94.14
PRK02224	880	chromosome segregation protein; Provisional	94.0
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	93.9
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	93.89
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	93.8
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	93.8
PF10186	302	Atg14: UV radiation resistance protein and autopha	93.74
PF14915	305	CCDC144C: CCDC144C protein coiled-coil region	93.61
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	93.6
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	93.34
PF05701	522	WEMBL: Weak chloroplast movement under blue light;	93.25
PRK02224	880	chromosome segregation protein; Provisional	93.22
PF05701	522	WEMBL: Weak chloroplast movement under blue light;	93.04
PRK01156	895	chromosome segregation protein; Provisional	92.99
KOG0933	1174	consensus Structural maintenance of chromosome pro	92.71
PF06818	202	Fez1: Fez1; InterPro: IPR009638 This family repres	92.67
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	92.38
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	92.35
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	92.35
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	92.32
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	92.12
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	91.81
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	91.75
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	91.74
PF14915	305	CCDC144C: CCDC144C protein coiled-coil region	91.55
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	91.47
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	91.38
PF09738	302	DUF2051: Double stranded RNA binding protein (DUF2	91.19
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	91.18
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	91.02
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	90.86
TIGR01005	754	eps_transp_fam exopolysaccharide transport protein	90.82
PRK10884	206	SH3 domain-containing protein; Provisional	90.73
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	90.38
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	90.01
PF00038	312	Filament: Intermediate filament protein; InterPro:	90.0
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	89.96
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	89.86
PRK01156	895	chromosome segregation protein; Provisional	89.84
PF10018	188	Med4: Vitamin-D-receptor interacting Mediator subu	89.49
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	89.4
PF06818	202	Fez1: Fez1; InterPro: IPR009638 This family repres	89.24
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	88.92
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	88.68
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	88.56
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	88.5
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	88.45
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	87.96
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	87.02
PF09763	701	Sec3_C: Exocyst complex component Sec3; InterPro:	87.01
TIGR01005	754	eps_transp_fam exopolysaccharide transport protein	86.85
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	86.65
PF05384	159	DegS: Sensor protein DegS; InterPro: IPR008595 Thi	86.43
PRK04778	569	septation ring formation regulator EzrA; Provision	85.9
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	85.85
PRK04863	1486	mukB cell division protein MukB; Provisional	85.81
cd07623	224	BAR_SNX1_2 The Bin/Amphiphysin/Rvs (BAR) domain of	85.78
PF09325	236	Vps5: Vps5 C terminal like; InterPro: IPR015404 Vp	85.72
KOG0933	1174	consensus Structural maintenance of chromosome pro	85.7
KOG0976	1265	consensus Rho/Rac1-interacting serine/threonine ki	85.68
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	85.56
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	85.44
PRK10884	206	SH3 domain-containing protein; Provisional	85.39
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	85.37
PF12795	240	MscS_porin: Mechanosensitive ion channel porin dom	85.01
PF12128	1201	DUF3584: Protein of unknown function (DUF3584); In	84.95
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	84.83
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	84.25
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	84.2
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	84.09
TIGR01010	362	BexC_CtrB_KpsE polysaccharide export inner-membran	84.0
KOG4673	961	consensus Transcription factor TMF, TATA element m	83.88
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	83.68
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	83.62
PRK04863	1486	mukB cell division protein MukB; Provisional	83.2
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	83.05
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	82.79
PRK04778	569	septation ring formation regulator EzrA; Provision	82.63
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	82.27
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	82.19
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	81.77
KOG0963	629	consensus Transcription factor/CCAAT displacement	81.76
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	81.02
KOG4438	446	consensus Centromere-associated protein NUF2 [Cell	80.98
cd07627	216	BAR_Vps5p The Bin/Amphiphysin/Rvs (BAR) domain of	80.93
TIGR01010	362	BexC_CtrB_KpsE polysaccharide export inner-membran	80.76
KOG0976	1265	consensus Rho/Rac1-interacting serine/threonine ki	80.52
PF08537	323	NBP1: Fungal Nap binding protein NBP1; InterPro: I	80.42
PF14988	206	DUF4515: Domain of unknown function (DUF4515)	80.35
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	80.21

>PRK11637 AmiB activator; Provisional

Probab=96.76  E-value=0.035  Score=53.96  Aligned_cols=54  Identities=17%  Similarity=0.236  Sum_probs=32.9

Q ss_pred             HHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHH
Q 022306          158 IKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFM  211 (299)
Q Consensus       158 ikStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm  211 (299)
                      |..++.+|......+.+.+..|..++.++-..+..+..++.++...+..+...+
T Consensus        77 l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~~rl  130 (428)
T PRK11637         77 LKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLAAQL  130 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555566666666666666666666666666666666666666666555443

>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=96.39  E-value=0.34  Score=43.34  Aligned_cols=78  Identities=22%  Similarity=0.326  Sum_probs=40.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDE-----LLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQ  176 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDe-----lLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKq  176 (299)
                      -+.++..++++.+.|+.++.+.=+     ....+...+.++......+..|+..+.....-|...+..+.+.+..|..+.
T Consensus        25 ~~~~l~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~r~~~l~~~i~~~~~~i~~~r~~l~~~~~~l~~~~  104 (302)
T PF10186_consen   25 LRSELQQLKEENEELRRRIEEILESDSNGQLLEIQQLKREIEELRERLERLRERIERLRKRIEQKRERLEELRESLEQRR  104 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355777777777777777666554     444444444444444444444444444444444444444444444444444


Q ss_pred             HHH
Q 022306          177 AAL  179 (299)
Q Consensus       177 AaL  179 (299)
                      ..|
T Consensus       105 ~~l  107 (302)
T PF10186_consen  105 SRL  107 (302)
T ss_pred             HHH
Confidence            333

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

>PF10174 Cast: RIM-binding protein of the cytomatrix active zone; InterPro: IPR019323 This entry represents a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion []

Probab=95.94  E-value=0.19  Score=53.82  Aligned_cols=111  Identities=24%  Similarity=0.234  Sum_probs=100.3

Q ss_pred             HHHHHHHHHHHHHh----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHH
Q 022306          108 ALREQVEDLQRKMF----EKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQ  183 (299)
Q Consensus       108 ~LreQVeeLqkKL~----EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKle  183 (299)
                      .|+..|.-|+..+.    ++|.+.+.++..........+++|.++.+|..|+.=|...|..|.++--...|++-=++.|.
T Consensus       249 ~le~Ei~~L~~~~~~~~~~r~~~~k~le~~~s~~~~mK~k~d~~~~eL~rk~~E~~~~qt~l~~~~~~~~d~r~hi~~lk  328 (775)
T PF10174_consen  249 DLEDEIYRLRSRGELSEADRDRLDKQLEVYKSHSLAMKSKMDRLKLELSRKKSELEALQTRLETLEEQDSDMRQHIEVLK  328 (775)
T ss_pred             HHHHHHHHHHhcccccccchHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            37888888877654    78999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          184 WEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       184 wE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      -.+-......+.||.|++.+++++-.=..++.+-+
T Consensus       329 esl~~ke~~~~~Lqsdve~Lr~rle~k~~~l~kk~  363 (775)
T PF10174_consen  329 ESLRAKEQEAEMLQSDVEALRFRLEEKNSQLEKKQ  363 (775)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999988777777555

Located at the C terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). These proteins also contain four coiled-coil domains [].

>PRK09039 hypothetical protein; Validated

Probab=95.92  E-value=0.38  Score=46.51  Aligned_cols=85  Identities=18%  Similarity=0.218  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhh-H---HH
Q 022306          134 KSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGE-M---SS  209 (299)
Q Consensus       134 ~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~e-I---ss  209 (299)
                      ..+...+.+++++++...++.-.-|.-++.|+..-+-+|+..+++|.-+|-.-.....+.++|+.+|...=.+ +   ..
T Consensus       115 ~~~~~~l~~~L~~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~~~~~~~l~~  194 (343)
T PRK09039        115 EGRAGELAQELDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVALAQRVQELNR  194 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3556666788999999999999999999999999999999999999999999988999999999998887533 4   44


Q ss_pred             HHHHH-hhhh
Q 022306          210 FMQIF-EGLI  218 (299)
Q Consensus       210 lm~~f-e~lt  218 (299)
                      |...| -.|.
T Consensus       195 ~~~~~~~~l~  204 (343)
T PRK09039        195 YRSEFFGRLR  204 (343)
T ss_pred             hHHHHHHHHH
Confidence            44333 4556

>PRK11637 AmiB activator; Provisional

Probab=95.80  E-value=0.2  Score=48.80  Aligned_cols=80  Identities=13%  Similarity=0.244  Sum_probs=33.8

Q ss_pred             cHHHHHHHHHHHHHHHHHHhh----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHH
Q 022306          102 EIEELVALREQVEDLQRKMFE----KDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQA  177 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~E----KDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqA  177 (299)
                      ..+++..++.||..+++++.+    ..++...++.+..++..++.+|+.+..++.+-+.-|..++.++.+++..+...+.
T Consensus        45 ~~~~l~~l~~qi~~~~~~i~~~~~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~  124 (428)
T PRK11637         45 NRDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQER  124 (428)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555666666665555542    2222233333333333333344444444433333333344444444444333333


Q ss_pred             HHHH
Q 022306          178 ALEK  181 (299)
Q Consensus       178 aLEK  181 (299)
                      .|.+
T Consensus       125 ~l~~  128 (428)
T PRK11637        125 LLAA  128 (428)
T ss_pred             HHHH
Confidence            3333

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=95.77  E-value=0.55  Score=49.30  Aligned_cols=29  Identities=10%  Similarity=0.243  Sum_probs=11.4

Q ss_pred             HHHHhhhHHHHHHHHHhhhhhhHHHHHHH
Q 022306          185 EAMTVSRKAEKLQEEVESMQGEMSSFMQI  213 (299)
Q Consensus       185 E~~~sn~Kve~Lq~dl~~m~~eIsslm~~  213 (299)
                      ++.....+.+.++.++..++.++..+...
T Consensus       890 ~~~~l~~~~~~l~~~~~~l~~~~~~~~~~  918 (1164)
T TIGR02169       890 ERDELEAQLRELERKIEELEAQIEKKRKR  918 (1164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333344444444444444433333

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.

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=95.63  E-value=0.66  Score=48.77  Aligned_cols=79  Identities=18%  Similarity=0.286  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          140 VHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       140 ~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      +...++.+..++.+.+.-+...+.++.+....+.+....+..+.-++..-..+++.++.++..++.++..+...++.+.
T Consensus       852 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~~~~l~~~~~~l~~~~~~l~~~~~~~~~~~~~l~~~~~~~~  930 (1164)
T TIGR02169       852 IEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEALE  930 (1164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444455555555555555555666666666666666666666666666666666555555544443

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.

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=95.28  E-value=1.8  Score=37.54  Aligned_cols=119  Identities=22%  Similarity=0.203  Sum_probs=109.6

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHhhhHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhh
Q 022306          100 EKEIEELVALREQVEDLQRKMFEKDELLK-----SLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLAD  174 (299)
Q Consensus       100 ~k~~eEl~~LreQVeeLqkKL~EKDelLk-----Sae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~Lad  174 (299)
                      .+-|-.+..|+.|+..++.+|..||++=.     --+++..+...+..+|||=..+|..=-..+.++-..|+..+-+|..
T Consensus         9 ~~~Rl~~~~lk~~l~k~~~ql~~ke~lge~L~~iDFeqLkien~~l~~kIeERn~eL~~Lk~~~~~~v~~L~h~keKl~~   88 (177)
T PF13870_consen    9 SKLRLKNITLKHQLAKLEEQLRQKEELGEGLHLIDFEQLKIENQQLNEKIEERNKELLKLKKKIGKTVQILTHVKEKLHF   88 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45677889999999999999999999844     4567789999999999999999988888899999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          175 KQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       175 KqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      ...-+..+.-++........+++.++.....+...+.....+|.
T Consensus        89 ~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~~~~~~~l~  132 (177)
T PF13870_consen   89 LSEELERLKQELKDREEELAKLREELYRVKKERDKLRKQNKKLR  132 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999987

>PRK09039 hypothetical protein; Validated

Probab=95.26  E-value=2.6  Score=40.84  Aligned_cols=29  Identities=10%  Similarity=0.121  Sum_probs=14.8

Q ss_pred             HHHHhHHhhHHHHhhhhHHHHHHHHHHHH
Q 022306          158 IKSTQLQLSDAKIKLADKQAALEKSQWEA  186 (299)
Q Consensus       158 ikStq~QLsdaki~LadKqAaLEKlewE~  186 (299)
                      +-+++.+|..++...++.++-++.|+-++
T Consensus       153 la~le~~L~~ae~~~~~~~~~i~~L~~~L  181 (343)
T PRK09039        153 LAALEAALDASEKRDRESQAKIADLGRRL  181 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555555555555555554443

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=95.13  E-value=1.2  Score=40.44  Aligned_cols=103  Identities=29%  Similarity=0.364  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHH
Q 022306          103 IEELVALREQVEDLQRKMFEKDELLKSLESSKS------------QVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKI  170 (299)
Q Consensus       103 ~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~------------em~a~~akvDELr~~laeKe~likStq~QLsdaki  170 (299)
                      ++.|...++++-++.++|.++|+-|..+.....            +-..+..+|+.+...+.++|.-|+.+.-+|     
T Consensus        74 r~~LR~~q~~~r~~~~klk~~~~el~k~~~~l~~L~~L~~dknL~eReeL~~kL~~~~~~l~~~~~ki~~Lek~l-----  148 (194)
T PF15619_consen   74 RERLRKSQEQERELERKLKDKDEELLKTKDELKHLKKLSEDKNLAEREELQRKLSQLEQKLQEKEKKIQELEKQL-----  148 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----
Confidence            445555556666777777777776665444321            222333333333333333333333322211     


Q ss_pred             hhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHh
Q 022306          171 KLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFE  215 (299)
Q Consensus       171 ~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe  215 (299)
                      .|+++     -..+++..-+.|+..++.++..++-||..|...+.
T Consensus       149 eL~~k-----~~~rql~~e~kK~~~~~~~~~~l~~ei~~L~~klk  188 (194)
T PF15619_consen  149 ELENK-----SFRRQLASEKKKHKEAQEEVKSLQEEIQRLNQKLK  188 (194)
T ss_pred             HHHhh-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            11111     15677888899999999999999999999887765

>PHA02562 46 endonuclease subunit; Provisional

Probab=95.03  E-value=0.7  Score=45.44  Aligned_cols=96  Identities=22%  Similarity=0.292  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHH
Q 022306          104 EELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQ  183 (299)
Q Consensus       104 eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKle  183 (299)
                      ..+..|..++.+|+.++.+=+..+..++....+.+.+..++.+++..+..+..-|.+...++...+       +.+++|+
T Consensus       299 ~~~~~l~d~i~~l~~~l~~l~~~i~~~~~~~~~~~~~~~~i~el~~~i~~~~~~i~~~~~~~~~l~-------~ei~~l~  371 (562)
T PHA02562        299 DRITKIKDKLKELQHSLEKLDTAIDELEEIMDEFNEQSKKLLELKNKISTNKQSLITLVDKAKKVK-------AAIEELQ  371 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHH
Confidence            466777778888888877777777777777777777777777777777776666655444444433       3344444


Q ss_pred             HHHHHhhhHHHHHHHHHhhhhhh
Q 022306          184 WEAMTVSRKAEKLQEEVESMQGE  206 (299)
Q Consensus       184 wE~~~sn~Kve~Lq~dl~~m~~e  206 (299)
                      -+....+.+...++.++..+..+
T Consensus       372 ~~~~~~~~~l~~l~~~l~~~~~~  394 (562)
T PHA02562        372 AEFVDNAEELAKLQDELDKIVKT  394 (562)
T ss_pred             hhhhchHHHHHHHHHHHHHHHHH
Confidence            33333333444444444444333

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=94.83  E-value=1.6  Score=45.53  Aligned_cols=13  Identities=0%  Similarity=-0.105  Sum_probs=6.2

Q ss_pred             HHHHHHHHHHHHH
Q 022306          251 MQRMEEAREAYIT  263 (299)
Q Consensus       251 ~~kmE~aR~aY~a  263 (299)
                      +..++.....+-+
T Consensus       967 ~~~l~~~i~~lg~  979 (1179)
T TIGR02168       967 EEEARRRLKRLEN  979 (1179)
T ss_pred             HHHHHHHHHHHHH
Confidence            4455554444444

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.

>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=94.73  E-value=2.7  Score=38.23  Aligned_cols=84  Identities=18%  Similarity=0.219  Sum_probs=63.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHH
Q 022306          135 SQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIF  214 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~f  214 (299)
                      +.......+|+.|..+|.+=...+..+..-+.++..+|.-...-|+.++-=+-....|+..|+.+|..+...+-+|-...
T Consensus        85 ~r~~~~eeri~~lE~~l~ea~~~~ee~e~k~~E~~rkl~~~E~~Le~aEeR~e~~E~ki~eLE~el~~~~~~lk~lE~~~  164 (237)
T PF00261_consen   85 NREQSDEERIEELEQQLKEAKRRAEEAERKYEEVERKLKVLEQELERAEERAEAAESKIKELEEELKSVGNNLKSLEASE  164 (237)
T ss_dssp             HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhHHHHHHHHHHHHHHHHHhhhhh
Confidence            44445566777777777777777777777777777888888888888888888888888888888888888777777666


Q ss_pred             hhhh
Q 022306          215 EGLI  218 (299)
Q Consensus       215 e~lt  218 (299)
                      ++..
T Consensus       165 ~~~~  168 (237)
T PF00261_consen  165 EKAS  168 (237)
T ss_dssp             HHHH
T ss_pred             hhhh
Confidence            6544

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 [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....

>cd07664 BAR_SNX2 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 2

Probab=94.67  E-value=2.2  Score=39.59  Aligned_cols=85  Identities=26%  Similarity=0.316  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHH------------HHHHHh----------HHhhHHHHhhhhHHHHHHHHHHHHHHhhhH
Q 022306          135 SQVNAVHLKLDELKRLAAEKDS------------LIKSTQ----------LQLSDAKIKLADKQAALEKSQWEAMTVSRK  192 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~------------likStq----------~QLsdaki~LadKqAaLEKlewE~~~sn~K  192 (299)
                      .++..++.+|.++....+..|.            +|.|+.          .+...+...|.-|++.++||.|-  .+..|
T Consensus        83 ~~laev~~ki~~~~~~qa~~d~~~l~e~L~eYiR~i~svK~~f~~R~k~~~~~~~a~~~L~kkr~~~~Kl~~~--~k~dK  160 (234)
T cd07664          83 SQLAEVEEKIDQLHQDQAFADFYLFSELLGDYIRLIAAVKGVFDQRMKCWQKWQDAQVTLQKKREAEAKLQYA--NKPDK  160 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc--CchhH
Confidence            5888999999999999999998            334432          36788999999999999999883  24679


Q ss_pred             HHHHHHHHhhhhhhHHHHHHHHhhhhhcC
Q 022306          193 AEKLQEEVESMQGEMSSFMQIFEGLIKND  221 (299)
Q Consensus       193 ve~Lq~dl~~m~~eIsslm~~fe~lt~n~  221 (299)
                      ++.++.+|...+.-.......|+.|+++.
T Consensus       161 ~~~~~~ev~~~e~~~~~a~~~fe~Is~~~  189 (234)
T cd07664         161 LQQAKDEIKEWEAKVQQGERDFEQISKTI  189 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999553

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX2 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures effcient cargo sorting by facilitating proper membrane localization

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

Probab=94.63  E-value=2  Score=39.54  Aligned_cols=105  Identities=15%  Similarity=0.253  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhH-----------HhhHHHHhhhhHHH
Q 022306          109 LREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQL-----------QLSDAKIKLADKQA  177 (299)
Q Consensus       109 LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~-----------QLsdaki~LadKqA  177 (299)
                      .+.+|++++.......+.+.++   +.++..+..+|+.|+.++..=.....++..           ++.+.+..++.+.+
T Consensus       193 y~~k~~~l~~~~~~~~~~~~~~---~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~le~~~~~~~~~~~~~i~~le~  269 (312)
T PF00038_consen  193 YQSKLEELRQQSEKSSEELESA---KEELKELRRQIQSLQAELESLRAKNASLERQLRELEQRLDEEREEYQAEIAELEE  269 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccccchh---HhHHHHHHhhhhHhhhhhhccccchhhhhhhHHHHHHHHHHHHHHHHHhhhccch
Confidence            3456666666665555444433   333344444444444333332222333333           33334455556666


Q ss_pred             HHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhh
Q 022306          178 ALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEG  216 (299)
Q Consensus       178 aLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~  216 (299)
                      -|.++.+++-.-..-...|-.-=-+|+.||.+.+.+|+|
T Consensus       270 el~~l~~~~~~~~~ey~~Ll~~K~~Ld~EIatYR~LLEg  308 (312)
T PF00038_consen  270 ELAELREEMARQLREYQELLDVKLALDAEIATYRKLLEG  308 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhC
Confidence            666666666666555566666556788899988888875

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 ....

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

Probab=94.59  E-value=1.6  Score=37.63  Aligned_cols=67  Identities=19%  Similarity=0.237  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHh
Q 022306          135 SQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVE  201 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~  201 (299)
                      ..+-.++.+|.-|-.+|..-+.-++.|.-.|.++.+......--+..|+-+...-.+|.+.|...+.
T Consensus        73 ~~~E~l~rriq~LEeele~ae~~L~e~~ekl~e~d~~ae~~eRkv~~le~~~~~~E~k~eel~~k~~  139 (143)
T PF12718_consen   73 SNAEQLNRRIQLLEEELEEAEKKLKETTEKLREADVKAEHFERKVKALEQERDQWEEKYEELEEKYK  139 (143)
T ss_pred             HhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence            3333555666666666666666666677777777666666666666666666666666666665554

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 [].

>PRK03918 chromosome segregation protein; Provisional

Probab=94.57  E-value=2.2  Score=44.50  Aligned_cols=106  Identities=13%  Similarity=0.280  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHH---hhHHHHhhhhHHHHHHHHH
Q 022306          107 VALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQ---LSDAKIKLADKQAALEKSQ  183 (299)
Q Consensus       107 ~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~Q---Lsdaki~LadKqAaLEKle  183 (299)
                      ..+..+++.|...+.+.+++.+.+..++.++..+.+.+.++..++...+..+...+.+   |..++..+...+..++.++
T Consensus       172 ~~~~~~~~~l~~~l~~l~~i~~~l~~l~~~~~~l~~ei~~l~~e~~~l~~~~~~~~~~l~~l~~~~~~~~~l~~~~~~l~  251 (880)
T PRK03918        172 KEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLE  251 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455566666666666666666666666666666666666666666666655555443   2333333344444444444


Q ss_pred             HHHHHhhhHHHHHHHHHhhhhhhHHHHHH
Q 022306          184 WEAMTVSRKAEKLQEEVESMQGEMSSFMQ  212 (299)
Q Consensus       184 wE~~~sn~Kve~Lq~dl~~m~~eIsslm~  212 (299)
                      -........+..++.++..++.++..+..
T Consensus       252 ~~~~~l~~~i~~l~~el~~l~~~l~~l~~  280 (880)
T PRK03918        252 GSKRKLEEKIRELEERIEELKKEIEELEE  280 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44333333344455554444444444333

>PRK03918 chromosome segregation protein; Provisional

Probab=94.51  E-value=7.2  Score=40.75  Aligned_cols=45  Identities=13%  Similarity=0.238  Sum_probs=28.5

Q ss_pred             hHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          174 DKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       174 dKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      +..+.++.++-+...-+.+...++.....+...|..+...++.|.
T Consensus       388 ~l~~~l~~l~~~~~~l~~~i~~l~~~~~~~~~~i~eL~~~l~~L~  432 (880)
T PRK03918        388 KLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELK  432 (880)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555556655555666666667777777777776666666665

>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=94.46  E-value=0.61  Score=52.32  Aligned_cols=112  Identities=21%  Similarity=0.355  Sum_probs=81.4

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhhHHHHHHHhHHhhHHHHhhhhHHHHHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLA-AEKDSLIKSTQLQLSDAKIKLADKQAALE  180 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~l-aeKe~likStq~QLsdaki~LadKqAaLE  180 (299)
                      |.+.+.-|++||++|.+++-+=   =+++-. ++++..++.+||++.... .-...=|++++.||---...++..+++++
T Consensus       856 d~~~l~~~~~~ie~l~kE~e~~---qe~~~K-k~~i~~lq~~i~~i~~e~~q~qk~kv~~~~~~~~~l~~~i~k~~~~i~  931 (1293)
T KOG0996|consen  856 DKKRLKELEEQIEELKKEVEEL---QEKAAK-KARIKELQNKIDEIGGEKVQAQKDKVEKINEQLDKLEADIAKLTVAIK  931 (1293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHH---HHhhhH-HHHHHHHHHHHHHhhchhhHHhHHHHHHHHHHHHHHHHHHHHhHHHHh
Confidence            5666777788888888877442   233333 688888888888887554 33455678888888888888888888888


Q ss_pred             HHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhh
Q 022306          181 KSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGL  217 (299)
Q Consensus       181 KlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~l  217 (299)
                      .-.|-+..--+++..|..+...++.++-.|+..+.++
T Consensus       932 ~s~~~i~k~q~~l~~le~~~~~~e~e~~~L~e~~~~~  968 (1293)
T KOG0996|consen  932 TSDRNIAKAQKKLSELEREIEDTEKELDDLTEELKGL  968 (1293)
T ss_pred             cCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            8777777777777777777777777777777666544

>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=94.36  E-value=1.7  Score=45.42  Aligned_cols=45  Identities=29%  Similarity=0.428  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Q 022306          109 LREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDS  156 (299)
Q Consensus       109 LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~  156 (299)
                      |+.|++..+   -|+++|++-...++.++..++..++.|+.+|.....
T Consensus       141 lQ~qlE~~q---kE~eeL~~~~~~Le~e~~~l~~~v~~l~~eL~~~~e  185 (546)
T PF07888_consen  141 LQNQLEECQ---KEKEELLKENEQLEEEVEQLREEVERLEAELEQEEE  185 (546)
T ss_pred             HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566666554   456667777777766666666666666666654433

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 [].

>KOG0243 consensus Kinesin-like protein [Cytoskeleton]

Probab=94.35  E-value=1.9  Score=48.05  Aligned_cols=182  Identities=20%  Similarity=0.238  Sum_probs=124.0

Q ss_pred             ccceeeecCCChhhhcccCC------CcccCCCCCCCCCcccCCCCCccc------cCCCCCCCCCCCcc-ccchhhhhh
Q 022306           33 RGSMIYTKTPSRESLLKKTT------DPKGRNAAQSLPPKRKKDNGDKDL------GKNANSNQDSDSFS-IFSSRALVS   99 (299)
Q Consensus        33 r~SmiYT~aP~resl~Kk~~------d~K~~k~~qs~p~Kk~rd~gd~dq------~k~~~~~q~~en~s-~~~s~~~~~   99 (299)
                      .-+||.|-.|+.-.|-.-.+      ..|.-+++.-++.|--++---||-      =|..-...+.-||- ++-++-.-.
T Consensus       360 KT~iIATiSPa~~~lEETlSTLEYA~RAKnIkNKPevNQkl~K~~llKd~~~EIerLK~dl~AaReKnGvyisee~y~~~  439 (1041)
T KOG0243|consen  360 KTCIIATISPAKHNLEETLSTLEYAHRAKNIKNKPEVNQKLMKKTLLKDLYEEIERLKRDLAAAREKNGVYISEERYTQE  439 (1041)
T ss_pred             eeEEEEEeCCCcccHHHHHHHHHHHHHhhhccCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhhCceEechHHHHHH
Confidence            56899999999665544333      235555555556443222111110      00000001122222 222222111


Q ss_pred             hhcHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhH
Q 022306          100 EKEIEELVALREQVEDLQRKMFEKDELLKSLESSKS----QVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADK  175 (299)
Q Consensus       100 ~k~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~----em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadK  175 (299)
                      +   .|.-...+||++|..+|..++..|+.+...-.    .-..++.+.+.++..|..+..-+.+++.++..++-.|..+
T Consensus       440 e---~e~~~~~~~ieele~el~~~~~~l~~~~e~~~~~~~~~~~l~~~~~~~k~~L~~~~~el~~~~ee~~~~~~~l~~~  516 (1041)
T KOG0243|consen  440 E---KEKKEMAEQIEELEEELENLEKQLKDLTELYMNQLEIKELLKEEKEKLKSKLQNKNKELESLKEELQQAKATLKEE  516 (1041)
T ss_pred             H---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            1   14667789999999999999999998877632    2246788999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhh
Q 022306          176 QAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGL  217 (299)
Q Consensus       176 qAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~l  217 (299)
                      .-.+-+++-=.++.-+-+.+||..++.++-++++|-..++..
T Consensus       517 e~ii~~~~~se~~l~~~a~~l~~~~~~s~~d~s~l~~kld~~  558 (1041)
T KOG0243|consen  517 EEIISQQEKSEEKLVDRATKLRRSLEESQDDLSSLFEKLDRK  558 (1041)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            988888777777777779999999999999999987666543

>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family

Probab=94.20  E-value=3.1  Score=38.88  Aligned_cols=17  Identities=6%  Similarity=0.204  Sum_probs=7.3

Q ss_pred             HhhhhhhHHHHHHHHhh
Q 022306          200 VESMQGEMSSFMQIFEG  216 (299)
Q Consensus       200 l~~m~~eIsslm~~fe~  216 (299)
                      +..++.++..+...++.
T Consensus       248 l~~~~~~l~~~~~~l~~  264 (423)
T TIGR01843       248 LTEAQARLAELRERLNK  264 (423)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            34444444444444443

Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.

>cd07665 BAR_SNX1 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1

Probab=94.17  E-value=2  Score=40.07  Aligned_cols=84  Identities=20%  Similarity=0.368  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHH------------HHHHh----------HHhhHHHHhhhhHHHHHHHHHHHHHHhhhH
Q 022306          135 SQVNAVHLKLDELKRLAAEKDSL------------IKSTQ----------LQLSDAKIKLADKQAALEKSQWEAMTVSRK  192 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~l------------ikStq----------~QLsdaki~LadKqAaLEKlewE~~~sn~K  192 (299)
                      +.+..++.+|.++....++.|.+            |.|+.          .+.++++..|.-|++.++||.|-  ....|
T Consensus        83 s~laev~~~i~~~~~~qa~qd~~~f~e~l~eYiRli~SVK~~f~~R~k~~~~~~~~~~~l~kKr~~~~Kl~~~--~~~dK  160 (234)
T cd07665          83 SQLAEVEEKIEQLHQEQANNDFFLLAELLADYIRLLSAVRGAFDQRMKTWQRWQDAQAMLQKKREAEARLLWA--NKPDK  160 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--CCchH
Confidence            58899999999999999998864            44442          46889999999999999999883  35689


Q ss_pred             HHHHHHHHhhhhhhHHHHHHHHhhhhhc
Q 022306          193 AEKLQEEVESMQGEMSSFMQIFEGLIKN  220 (299)
Q Consensus       193 ve~Lq~dl~~m~~eIsslm~~fe~lt~n  220 (299)
                      +..++.||...+..+..+..-|+.|+++
T Consensus       161 ~~~a~~Ev~e~e~k~~~a~~~fe~is~~  188 (234)
T cd07665         161 LQQAKDEIAEWESRVTQYERDFERISAT  188 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999944

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX1 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures effcient cargo sorting by facilitating proper membrane localization

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]

Probab=94.16  E-value=3  Score=46.08  Aligned_cols=10  Identities=40%  Similarity=0.368  Sum_probs=6.6

Q ss_pred             HHHHHHHHhh
Q 022306          260 AYITAVAMAK  269 (299)
Q Consensus       260 aY~aAvaaAK  269 (299)
                      .|..||.+|=
T Consensus       530 ~y~~Aie~al  539 (1163)
T COG1196         530 KYETALEAAL  539 (1163)
T ss_pred             HHHHHHHHHc
Confidence            5777776664

>PHA02562 46 endonuclease subunit; Provisional

Probab=94.14  E-value=1.5  Score=43.09  Aligned_cols=28  Identities=18%  Similarity=0.031  Sum_probs=19.2

Q ss_pred             CCCCCChHHHHHHHHHHHHHHHHHHHhh
Q 022306          242 DIDDLDDVEMQRMEEAREAYITAVAMAK  269 (299)
Q Consensus       242 ~~d~~~~~e~~kmE~aR~aY~aAvaaAK  269 (299)
                      +...++.-+.+++-.|+.....+++..+
T Consensus       465 ~~~~lS~Ge~~r~~la~~l~~~~~~~~~  492 (562)
T PHA02562        465 SYASFSQGEKARIDLALLFTWRDVASKV  492 (562)
T ss_pred             ChhhcChhHHHHHHHHHHHHHHHHHHHh
Confidence            3456677778888888777766666644

>PRK02224 chromosome segregation protein; Provisional

Probab=94.00  E-value=1.7  Score=45.45  Aligned_cols=46  Identities=17%  Similarity=0.314  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022306          105 ELVALREQVEDLQRKMFEK--DELLKSLESSKSQVNAVHLKLDELKRL  150 (299)
Q Consensus       105 El~~LreQVeeLqkKL~EK--DelLkSae~~~~em~a~~akvDELr~~  150 (299)
                      -...++.|+++|+..|.++  ..+...+.....++..+...+++++..
T Consensus       181 ~~~~~~~~~~~~~~~l~~~~~~~l~~~l~~~~~~l~el~~~i~~~~~~  228 (880)
T PRK02224        181 VLSDQRGSLDQLKAQIEEKEEKDLHERLNGLESELAELDEEIERYEEQ  228 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6677788888888888776  334444444444444444444443333

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

Probab=93.90  E-value=2.1  Score=47.68  Aligned_cols=117  Identities=21%  Similarity=0.305  Sum_probs=83.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH----------------------------------------------HH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESS----------------------------------------------KS  135 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~----------------------------------------------~~  135 (299)
                      ..+++...++.+..||.++.++-.-..++.+.                                              .+
T Consensus       286 ~~~~i~~~qek~~~l~~ki~~~~~k~~~~r~k~teiea~i~~~~~e~~~~d~Ei~~~r~~~~~~~re~~~~~~~~~~~~n  365 (1074)
T KOG0250|consen  286 QEEEIKKKQEKVDTLQEKIEEKQGKIEEARQKLTEIEAKIGELKDEVDAQDEEIEEARKDLDDLRREVNDLKEEIREIEN  365 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44566666666666666666666666665522                                              17


Q ss_pred             HHHHHHHHHHHHHHHHHhh-HHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhh-------HHHHHHHHHhhhhhhH
Q 022306          136 QVNAVHLKLDELKRLAAEK-DSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSR-------KAEKLQEEVESMQGEM  207 (299)
Q Consensus       136 em~a~~akvDELr~~laeK-e~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~-------Kve~Lq~dl~~m~~eI  207 (299)
                      .|.++...+|.+++++++= ..+.++++.++.+..-++...+-.+|++|-.+..-..       ++...++++++.+.+|
T Consensus       366 ~i~~~k~~~d~l~k~I~~~~~~~~~~~~~~~~e~e~k~~~L~~evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i  445 (1074)
T KOG0250|consen  366 SIRKLKKEVDRLEKQIADLEKQTNNELGSELEERENKLEQLKKEVEKLEEQINSLREELNEVKEKAKEEEEEKEHIEGEI  445 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            7888888889999988874 4455999999999999999999999988875554444       4445566666677777


Q ss_pred             HHHHHHHhhhh
Q 022306          208 SSFMQIFEGLI  218 (299)
Q Consensus       208 sslm~~fe~lt  218 (299)
                      .++....+.++
T Consensus       446 ~~l~k~i~~~~  456 (1074)
T KOG0250|consen  446 LQLRKKIENIS  456 (1074)
T ss_pred             HHHHHHHHHHH
Confidence            77777766555

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

Probab=93.89  E-value=4  Score=38.94  Aligned_cols=60  Identities=22%  Similarity=0.286  Sum_probs=46.6

Q ss_pred             HHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhh
Q 022306          157 LIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEG  216 (299)
Q Consensus       157 likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~  216 (299)
                      -+..+..+|...+..++.++..|+.++-+....+.+++.+.++...+..+|..+..+.++
T Consensus       210 eL~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~  269 (325)
T PF08317_consen  210 ELEALRQELAEQKEEIEAKKKELAELQEELEELEEKIEELEEQKQELLAEIAEAEKIREE  269 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355667777777777788888888888888888888888888888888888877766653

>smart00787 Spc7 Spc7 kinetochore protein

Probab=93.80  E-value=2.6  Score=40.71  Aligned_cols=83  Identities=19%  Similarity=0.241  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHH----HHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHH
Q 022306          134 KSQVNAVHLKLDELKRLAAEKDS----LIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSS  209 (299)
Q Consensus       134 ~~em~a~~akvDELr~~laeKe~----likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIss  209 (299)
                      ...-+.+..++..|++...+-+.    .+..+..+|......+..|+.-++.++-++...+.+++...++...++.+|..
T Consensus       178 ~~~~~~L~~e~~~L~~~~~e~~~~d~~eL~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I~~  257 (312)
T smart00787      178 RDRKDALEEELRQLKQLEDELEDCDPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIAE  257 (312)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35566677777777777777544    67777778888888888888888888888888888888888888888888877


Q ss_pred             HHHHHhh
Q 022306          210 FMQIFEG  216 (299)
Q Consensus       210 lm~~fe~  216 (299)
                      ...+++.
T Consensus       258 ae~~~~~  264 (312)
T smart00787      258 AEKKLEQ  264 (312)
T ss_pred             HHHHHHh
Confidence            7776653

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

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

Probab=93.80  E-value=5  Score=36.30  Aligned_cols=113  Identities=15%  Similarity=0.362  Sum_probs=89.0

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhH
Q 022306          100 EKEIEELVALREQVEDLQRKMFEKDELLKSLES----SKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADK  175 (299)
Q Consensus       100 ~k~~eEl~~LreQVeeLqkKL~EKDelLkSae~----~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadK  175 (299)
                      -.+-+-+..|.+||.+++++....+-.+..+..    +..-+..+...+++|++++..=+    .-...|..++..+...
T Consensus        23 ~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~y~----kdK~~L~~~k~rl~~~   98 (201)
T PF13851_consen   23 LNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKNYE----KDKQSLQNLKARLKEL   98 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH
Confidence            345567889999999999998888777665544    35677788999999999998633    4455788899999999


Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHH-HHHHHHhh
Q 022306          176 QAALEKSQWEAMTVSRKAEKLQEEVESMQGEMS-SFMQIFEG  216 (299)
Q Consensus       176 qAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIs-slm~~fe~  216 (299)
                      +--|..|+||-=.-..++.+++.+-+.+..-+- ++..+.++
T Consensus        99 ek~l~~Lk~e~evL~qr~~kle~ErdeL~~kf~~~i~evqQk  140 (201)
T PF13851_consen   99 EKELKDLKWEHEVLEQRFEKLEQERDELYRKFESAIQEVQQK  140 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999888875544 44444443

>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=93.74  E-value=4.9  Score=36.00  Aligned_cols=107  Identities=18%  Similarity=0.325  Sum_probs=67.4

Q ss_pred             cHHHHHHHHHHHHHHHH-----HHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhh---
Q 022306          102 EIEELVALREQVEDLQR-----KMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLA---  173 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqk-----KL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~La---  173 (299)
                      -+.+...|+.+|+++=.     ..+....+-..++....++..+...++.+++++.++-..|...+.+|...+..|.   
T Consensus        32 ~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~r~~~l~~~i~~~~~~i~~~r~~l~~~~~~l~~~~~~l~~~~  111 (302)
T PF10186_consen   32 LKEENEELRRRIEEILESDSNGQLLEIQQLKREIEELRERLERLRERIERLRKRIEQKRERLEELRESLEQRRSRLSASQ  111 (302)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34566677777777655     6666666666666667777777777777777777777777777777766666665   


Q ss_pred             ----hHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHH
Q 022306          174 ----DKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMS  208 (299)
Q Consensus       174 ----dKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIs  208 (299)
                          .....++++.-++-....++..++..+..-+..+-
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~~r~~l~  150 (302)
T PF10186_consen  112 DLVESRQEQLEELQNELEERKQRLSQLQSQLARRRRQLI  150 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                22233444444555555555566666666555544

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

>PF14915 CCDC144C: CCDC144C protein coiled-coil region

Probab=93.61  E-value=3.5  Score=40.43  Aligned_cols=85  Identities=20%  Similarity=0.250  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHH
Q 022306          134 KSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQI  213 (299)
Q Consensus       134 ~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~  213 (299)
                      ....|.+..++-..+-.|.||--++.++|-.|+.++-.+-++..+..--+--+-+.--|-+.|++-|..++.|-..|+++
T Consensus       157 esK~nsLe~elh~trdaLrEKtL~lE~~QrdL~Qtq~q~KE~e~m~qne~~kv~k~~~Kqes~eERL~QlqsEN~LLrQQ  236 (305)
T PF14915_consen  157 ESKFNSLEIELHHTRDALREKTLALESVQRDLSQTQCQIKEIEHMYQNEQDKVNKYIGKQESLEERLSQLQSENMLLRQQ  236 (305)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555566666666666666666666666666666555555555666678899999999999999999999


Q ss_pred             Hhhhh
Q 022306          214 FEGLI  218 (299)
Q Consensus       214 fe~lt  218 (299)
                      ++..-
T Consensus       237 LddA~  241 (305)
T PF14915_consen  237 LDDAH  241 (305)
T ss_pred             HHHHH
Confidence            98544

>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family

Probab=93.60  E-value=2.4  Score=39.60  Aligned_cols=27  Identities=4%  Similarity=0.104  Sum_probs=20.8

Q ss_pred             hhHHHHHHHHHhhhhhhHHHHHHHHhh
Q 022306          190 SRKAEKLQEEVESMQGEMSSFMQIFEG  216 (299)
Q Consensus       190 n~Kve~Lq~dl~~m~~eIsslm~~fe~  216 (299)
                      ..+...++.++..++.++..+...++.
T Consensus       245 ~~~l~~~~~~l~~~~~~l~~~~~~l~~  271 (423)
T TIGR01843       245 LEELTEAQARLAELRERLNKARDRLQR  271 (423)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            345677888888888888888777663

Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.

>PF10174 Cast: RIM-binding protein of the cytomatrix active zone; InterPro: IPR019323 This entry represents a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion []

Probab=93.34  E-value=3.6  Score=44.53  Aligned_cols=114  Identities=26%  Similarity=0.325  Sum_probs=74.3

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHH-------------------------HHHHHHHHHHHHHHHHHHHhhHHHHH
Q 022306          105 ELVALREQVEDLQRKMFEKDELLKSLESS-------------------------KSQVNAVHLKLDELKRLAAEKDSLIK  159 (299)
Q Consensus       105 El~~LreQVeeLqkKL~EKDelLkSae~~-------------------------~~em~a~~akvDELr~~laeKe~lik  159 (299)
                      +-..|+..|+.|.-+|-+|...|.-....                         ..+++.++++||.|..+|.+||..+.
T Consensus       337 ~~~~Lqsdve~Lr~rle~k~~~l~kk~~~~~~~qeE~~~~~~Ei~~l~d~~d~~e~ki~~Lq~kie~Lee~l~ekd~ql~  416 (775)
T PF10174_consen  337 EAEMLQSDVEALRFRLEEKNSQLEKKQAQIEKLQEEKSRLQGEIEDLRDMLDKKERKINVLQKKIENLEEQLREKDRQLD  416 (775)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34567888899999999998888654432                         26889999999999999999999887


Q ss_pred             HHhHHhh---------HH----HHhhhhH------------------HHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHH
Q 022306          160 STQLQLS---------DA----KIKLADK------------------QAALEKSQWEAMTVSRKAEKLQEEVESMQGEMS  208 (299)
Q Consensus       160 Stq~QLs---------da----ki~LadK------------------qAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIs  208 (299)
                      ....-|.         .+    ..-++++                  +--++..+.|+..-..+++.||.+|+..+..+.
T Consensus       417 ~~k~Rl~~~~d~~~~~~~~~~lEea~~eker~~e~l~e~r~~~e~e~~Eele~~~~e~~~lk~~~~~LQ~eLsEk~~~l~  496 (775)
T PF10174_consen  417 EEKERLSSQADSSNEDEALETLEEALREKERLQERLEEQRERAEKERQEELETYQKELKELKAKLESLQKELSEKELQLE  496 (775)
T ss_pred             HHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence            7776666         11    1122233                  223344555556666666666666666655444


Q ss_pred             HHHHHHhhhh
Q 022306          209 SFMQIFEGLI  218 (299)
Q Consensus       209 slm~~fe~lt  218 (299)
                      .+..-.-+++
T Consensus       497 ~~kee~s~l~  506 (775)
T PF10174_consen  497 DAKEEASKLA  506 (775)
T ss_pred             HhhhHHHHHh
Confidence            4444444454

Located at the C terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). These proteins also contain four coiled-coil domains [].

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

Probab=93.25  E-value=5.4  Score=40.66  Aligned_cols=107  Identities=25%  Similarity=0.345  Sum_probs=83.5

Q ss_pred             HHHHHHHHHHHHHHHHH----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhh-------
Q 022306          104 EELVALREQVEDLQRKM----FEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKL-------  172 (299)
Q Consensus       104 eEl~~LreQVeeLqkKL----~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~L-------  172 (299)
                      ..+.....++++.+..|    .|-..+-.+++++..++.-....+..++.....-...|.+++.+|...+..|       
T Consensus       281 ~~l~s~~~ELe~ak~~L~~~k~E~~~L~~~vesL~~ELe~~K~el~~lke~e~~a~~~v~~L~~eL~~~r~eLea~~~~e  360 (522)
T PF05701_consen  281 SSLASAKKELEEAKKELEKAKEEASSLRASVESLRSELEKEKEELERLKEREKEASSEVSSLEAELNKTRSELEAAKAEE  360 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhHHHHHHHHHHHHHHHHhhh
Confidence            34666777777766666    4666777888889999999999999999999999999999998888777766       


Q ss_pred             -------hhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHH
Q 022306          173 -------ADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSF  210 (299)
Q Consensus       173 -------adKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIssl  210 (299)
                             .++...|+++--|+-.-...++.++.++..+..+|...
T Consensus       361 ~~~k~~~~~l~~~Lqql~~Eae~Ak~ea~~~~~E~~~~k~E~e~~  405 (522)
T PF05701_consen  361 EKAKEAMSELPKALQQLSSEAEEAKKEAEEAKEEVEKAKEEAEQT  405 (522)
T ss_pred             cchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                   45667788888787777777777777777777776644

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

>PRK02224 chromosome segregation protein; Provisional

Probab=93.22  E-value=2.9  Score=43.86  Aligned_cols=12  Identities=17%  Similarity=-0.039  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHhh
Q 022306          258 REAYITAVAMAK  269 (299)
Q Consensus       258 R~aY~aAvaaAK  269 (299)
                      ...|-.++..++
T Consensus       435 ~~~~~~~l~~~~  446 (880)
T PRK02224        435 LRTARERVEEAE  446 (880)
T ss_pred             HHHHHHHHHHHH
Confidence            334444444444

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

Probab=93.04  E-value=5.4  Score=40.66  Aligned_cols=111  Identities=23%  Similarity=0.314  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH---hhHHHHHHHhHHhhHHHHhhhhHHHHHH
Q 022306          105 ELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKR-LAA---EKDSLIKSTQLQLSDAKIKLADKQAALE  180 (299)
Q Consensus       105 El~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~-~la---eKe~likStq~QLsdaki~LadKqAaLE  180 (299)
                      +|..-.+.|+.|...+.....+=.-+.....++..+++.|...+. .+.   +........+..|..++..|.+.+..|+
T Consensus       219 ~leeae~~l~~L~~e~~~~k~Le~kL~~a~~~l~~Lq~El~~~~~~~l~~~~~~~~~~~~~~~~l~s~~~ELe~ak~~L~  298 (522)
T PF05701_consen  219 ELEEAEEELEELKEELEAAKDLESKLAEASAELESLQAELEAAKESKLEEEAEAKEKSSELQSSLASAKKELEEAKKELE  298 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHhhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence            444455555555555522222222233334444444444444433 111   1223344455557777777777788888


Q ss_pred             HHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHh
Q 022306          181 KSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFE  215 (299)
Q Consensus       181 KlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe  215 (299)
                      +..-|+..-...|+.|+.+|.....+|..+..-..
T Consensus       299 ~~k~E~~~L~~~vesL~~ELe~~K~el~~lke~e~  333 (522)
T PF05701_consen  299 KAKEEASSLRASVESLRSELEKEKEELERLKEREK  333 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888888888888888888777777665443

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

>PRK01156 chromosome segregation protein; Provisional

Probab=92.99  E-value=11  Score=39.97  Aligned_cols=72  Identities=15%  Similarity=0.209  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhh
Q 022306          130 LESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVES  202 (299)
Q Consensus       130 ae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~  202 (299)
                      ++....+...+..+++.++..+++.+.-+.....++...+-.+...+-++++++-=-+. ...+..++.-++.
T Consensus       676 ~~~~~~~~~~l~~~l~~l~~~~~~l~~~i~~l~~~~~~l~eel~~~~~~~~~l~~~~~~-~~~l~~~r~~l~k  747 (895)
T PRK01156        676 INDIEDNLKKSRKALDDAKANRARLESTIEILRTRINELSDRINDINETLESMKKIKKA-IGDLKRLREAFDK  747 (895)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHhhh
Confidence            34445566666667777777777777777777777666666666555555543332111 1134456665654

>KOG0933 consensus Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=92.71  E-value=4.4  Score=45.37  Aligned_cols=32  Identities=31%  Similarity=0.470  Sum_probs=23.9

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESS  133 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~  133 (299)
                      .-+++-.+.+.|++++..+-|++.+++..+.-
T Consensus       739 ~~~~~~~~~e~v~e~~~~Ike~~~~~k~~~~~  770 (1174)
T KOG0933|consen  739 LLDDLKELLEEVEESEQQIKEKERALKKCEDK  770 (1174)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34567777888888888888888888776654

>PF06818 Fez1: Fez1; InterPro: IPR009638 This family represents the eukaryotic Fez1 protein

Probab=92.67  E-value=2.9  Score=38.77  Aligned_cols=96  Identities=26%  Similarity=0.341  Sum_probs=73.4

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHH
Q 022306          105 ELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQW  184 (299)
Q Consensus       105 El~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlew  184 (299)
                      ||.-|.-|+-|.|-.+.-|+          ++|..+.+.+-+++..+..++.-+..++.       .+-.|++.||..|-
T Consensus        11 EIsLLKqQLke~q~E~~~K~----------~Eiv~Lr~ql~e~~~~l~~~~~~~~~l~~-------~~~~K~~ELE~ce~   73 (202)
T PF06818_consen   11 EISLLKQQLKESQAEVNQKD----------SEIVSLRAQLRELRAELRNKESQIQELQD-------SLRTKQLELEVCEN   73 (202)
T ss_pred             hHHHHHHHHHHHHHHHHHHH----------hHHHHHHHHHHHHHHHHHhhHHHHHHHHH-------HHHHhhHhHHHhHH
Confidence            67777777777777776665          45666666666666666666665555444       44568888999999


Q ss_pred             HHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhh
Q 022306          185 EAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGL  217 (299)
Q Consensus       185 E~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~l  217 (299)
                      |+-.....++-|++.++.+..||..|..-+..+
T Consensus        74 ELqr~~~Ea~lLrekl~~le~El~~Lr~~l~~~  106 (202)
T PF06818_consen   74 ELQRKKNEAELLREKLGQLEAELAELREELACA  106 (202)
T ss_pred             HHHHHhCHHHHhhhhhhhhHHHHHHHHHHHHhh
Confidence            998888888999999999999999999888876

Fez1 contains a leucine-zipper region with similarity to the DNA-binding domain of the cAMP-responsive activating-transcription factor 5 []. There is evidence that Fez1 inhibits cancer cell growth through regulation of mitosis, and that its alterations result in abnormal cell growth []. Note that some family members contain more than one copy of this region.; GO: 0005737 cytoplasm, 0016020 membrane

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

Probab=92.38  E-value=10  Score=35.92  Aligned_cols=48  Identities=17%  Similarity=0.259  Sum_probs=31.5

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAA  152 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~la  152 (299)
                      .+++|..++++++.+.+.+.+++..++.+   .+++..+...|++++.+..
T Consensus        29 ~~~~l~k~~~e~e~~~~~~~~~~~e~e~l---e~qv~~~e~ei~~~r~r~~   76 (239)
T COG1579          29 IRKALKKAKAELEALNKALEALEIELEDL---ENQVSQLESEIQEIRERIK   76 (239)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
Confidence            56678888888888888887776655544   4455555555655555544

>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=92.35  E-value=7  Score=36.48  Aligned_cols=102  Identities=17%  Similarity=0.327  Sum_probs=83.3

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHH
Q 022306          106 LVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWE  185 (299)
Q Consensus       106 l~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE  185 (299)
                      |..|+.++.+|++.   |.+++..++.+.++=.-|..--.|+...+.||.+++.    +|..-+.+...+.+-+-.++.|
T Consensus         3 i~~ir~K~~~lek~---k~~i~~e~~~~e~ee~~L~e~~kE~~~L~~Er~~h~e----eLrqI~~DIn~lE~iIkqa~~e   75 (230)
T PF10146_consen    3 IKEIRNKTLELEKL---KNEILQEVESLENEEKCLEEYRKEMEELLQERMAHVE----ELRQINQDINTLENIIKQAESE   75 (230)
T ss_pred             HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHH
Confidence            56678888888876   5678888888887777777777777777889988886    6777888888888888888888


Q ss_pred             HHHhhhHHHHHHHHHhhhhhhHHHHHHHH
Q 022306          186 AMTVSRKAEKLQEEVESMQGEMSSFMQIF  214 (299)
Q Consensus       186 ~~~sn~Kve~Lq~dl~~m~~eIsslm~~f  214 (299)
                      -...-.++..+++++.-|..+|-.++.-+
T Consensus        76 r~~~~~~i~r~~eey~~Lk~~in~~R~e~  104 (230)
T PF10146_consen   76 RNKRQEKIQRLYEEYKPLKDEINELRKEY  104 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888889888888888888887763

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.

>TIGR00606 rad50 rad50

Probab=92.35  E-value=5  Score=44.86  Aligned_cols=133  Identities=14%  Similarity=0.120  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhh-------hhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhH
Q 022306          135 SQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKL-------ADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEM  207 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~likStq~QLsdaki~L-------adKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eI  207 (299)
                      +......++++-+++++.+|..-|+.+-....+.=..+       -..+-++.+++.++-.-+.++..++.++..+++.+
T Consensus       528 ~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~el~~~~~~~~~~~~el~~~e~~l  607 (1311)
T TIGR00606       528 NHHTTTRTQMEMLTKDKMDKDEQIRKIKSRHSDELTSLLGYFPNKKQLEDWLHSKSKEINQTRDRLAKLNKELASLEQNK  607 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55666778888888888888888877666654333222       22344555555555555555555555555554444


Q ss_pred             -------HHHHHHHhhhhhcCCCCCCCCCCCCCcccccccCCCC--CCChHHHHHHHHHHHHHHHHHHHh--hhcC
Q 022306          208 -------SSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDID--DLDDVEMQRMEEAREAYITAVAMA--KEKQ  272 (299)
Q Consensus       208 -------sslm~~fe~lt~n~S~~~~~~d~d~~p~~~d~l~~~d--~~~~~e~~kmE~aR~aY~aAvaaA--Kenp  272 (299)
                             ..+...++...++..     ++|++.+|+-.-...-+  +.-..+....+-....|-.++..|  +.+|
T Consensus       608 ~~~~~~l~~~~~eL~~~~~~i~-----~~~~~~~~~~~L~~~~~~l~~~~~~~~~~~~~~~~~~k~ie~a~~~~~~  678 (1311)
T TIGR00606       608 NHINNELESKEEQLSSYEDKLF-----DVCGSQDEESDLERLKEEIEKSSKQRAMLAGATAVYSQFITQLTDENQS  678 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHh-----cCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC
Confidence                   444455554444333     34444444321111101  111222333444448899999999  6443

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

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=92.32  E-value=4.1  Score=48.07  Aligned_cols=79  Identities=19%  Similarity=0.302  Sum_probs=67.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHH
Q 022306          135 SQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQI  213 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~  213 (299)
                      .++..+...+++...+.++.+.-.+..+..+.+-+..+.|....+.|++.|.-...+++..|++++..++-.|+.|..-
T Consensus       908 ~~l~~~~~~~e~~ee~~~~le~~~~~~~~e~~~l~~~~~~~E~~~~k~~~Ek~~~e~~~~~l~~e~~~~~e~~~kL~ke  986 (1930)
T KOG0161|consen  908 KELKELKERLEEEEEKNAELERKKRKLEQEVQELKEQLEELELTLQKLELEKNAAENKLKNLEEEINSLDENISKLSKE  986 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6677777778888888888888888888888888888999999999999999999999999999999988888877643

>TIGR00606 rad50 rad50

Probab=92.12  E-value=2.9  Score=46.63  Aligned_cols=70  Identities=14%  Similarity=0.277  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHhhHHHHHHH---hHHhhHHHHhhh
Q 022306          104 EELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDEL-------KRLAAEKDSLIKST---QLQLSDAKIKLA  173 (299)
Q Consensus       104 eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDEL-------r~~laeKe~likSt---q~QLsdaki~La  173 (299)
                      .|+..|+.||++|..++..-..- .+++.+..++..+..+++.+       ..+...+..-|..+   ..++.+.+.+++
T Consensus       799 ~ei~~l~~qie~l~~~l~~~~~~-~s~~ele~ei~~~~~el~~l~~~~e~l~~e~e~~~~eI~~Lq~ki~el~~~klkl~  877 (1311)
T TIGR00606       799 MELKDVERKIAQQAAKLQGSDLD-RTVQQVNQEKQEKQHELDTVVSKIELNRKLIQDQQEQIQHLKSKTNELKSEKLQIG  877 (1311)
T ss_pred             HHHHHHHHHHHHHHHHhcccccc-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555554444433221 24444444444444444444       55555555555555   333344444444


Q ss_pred             h
Q 022306          174 D  174 (299)
Q Consensus       174 d  174 (299)
                      +
T Consensus       878 ~  878 (1311)
T TIGR00606       878 T  878 (1311)
T ss_pred             H
Confidence            4

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

>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=91.81  E-value=2.2  Score=38.81  Aligned_cols=62  Identities=21%  Similarity=0.266  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH------------------HHHHHHHHHHHHHHHHhhHHHHHHHhHH
Q 022306          103 IEELVALREQVEDLQRKMFEKDELLKSLESSKSQ------------------VNAVHLKLDELKRLAAEKDSLIKSTQLQ  164 (299)
Q Consensus       103 ~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~e------------------m~a~~akvDELr~~laeKe~likStq~Q  164 (299)
                      +.++-...++++.++.+|-+.+.-+..++.-..-                  +..+..+++++.+.+-+-+.-++.+...
T Consensus         7 ~~eld~~~~~~~~~~~~l~~~~~~~~~aE~e~~~l~rri~~lE~~le~~eerL~~~~~kL~~~e~~~de~er~~k~lE~r   86 (237)
T PF00261_consen    7 KDELDEAEERLEEAEEKLKEAEKRAEKAEAEVASLQRRIQLLEEELERAEERLEEATEKLEEAEKRADESERARKVLENR   86 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            4567777778888888887777766666554311                  1123445555555555555555554443

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 [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....

>KOG0980 consensus Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton]

Probab=91.75  E-value=6.5  Score=43.49  Aligned_cols=52  Identities=23%  Similarity=0.254  Sum_probs=28.2

Q ss_pred             HHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          167 DAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       167 daki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      +..-..+++.-.||+++++.=.-++|.++...-+++++.|...+.-.|+.+.
T Consensus       463 ~~~~~~~~L~d~le~~~~~~~~~~~K~e~~~~~le~l~~El~~l~~e~~~lq  514 (980)
T KOG0980|consen  463 DVEEENTNLNDQLEELQRAAGRAETKTESQAKALESLRQELALLLIELEELQ  514 (980)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444455555556666655555555555555555555555555555555444

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]

Probab=91.74  E-value=7.2  Score=43.18  Aligned_cols=70  Identities=19%  Similarity=0.313  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhh
Q 022306          135 SQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQ  204 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~  204 (299)
                      .++..+..+++++..++..=+.-+...+.++...+..+...++.+..++-++.....+.+.|+..+..+.
T Consensus       828 ~ei~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~l~~~~~~~~~l~~~l~~~~  897 (1163)
T COG1196         828 QEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELE  897 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444443333333444444444444444444444444444444444444444433333

>PF14915 CCDC144C: CCDC144C protein coiled-coil region

Probab=91.55  E-value=13  Score=36.54  Aligned_cols=83  Identities=18%  Similarity=0.248  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHH
Q 022306          135 SQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIF  214 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~f  214 (299)
                      .+|+.+...-+-|-++|+.=++=+.|+.-+||.+.--|.+|-.+||-+|+++-..-+..-.|+.-.-+=++.++.++..-
T Consensus       137 ~d~S~lkd~ne~LsQqLskaesK~nsLe~elh~trdaLrEKtL~lE~~QrdL~Qtq~q~KE~e~m~qne~~kv~k~~~Kq  216 (305)
T PF14915_consen  137 SDVSNLKDNNEILSQQLSKAESKFNSLEIELHHTRDALREKTLALESVQRDLSQTQCQIKEIEHMYQNEQDKVNKYIGKQ  216 (305)
T ss_pred             chHHhHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            46777788888899999999999999999999999999999999999999999999999988888888888888777655


Q ss_pred             hhh
Q 022306          215 EGL  217 (299)
Q Consensus       215 e~l  217 (299)
                      +.+
T Consensus       217 es~  219 (305)
T PF14915_consen  217 ESL  219 (305)
T ss_pred             HHH
Confidence            433

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

Probab=91.47  E-value=1.7  Score=38.50  Aligned_cols=48  Identities=19%  Similarity=0.220  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHH
Q 022306          135 SQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKS  182 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKl  182 (299)
                      .+...+..++..|...+.+|...+..++.++.--++.+.-...-+.+|
T Consensus       123 ~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l  170 (194)
T PF08614_consen  123 AELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQLNMLEEKLRKL  170 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444445555555555555554444444444443333333333

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.

>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=91.38  E-value=10  Score=39.73  Aligned_cols=30  Identities=23%  Similarity=0.185  Sum_probs=15.4

Q ss_pred             eeecCCChhh-hcccCCCcccCCCCCCCCCcc
Q 022306           37 IYTKTPSRES-LLKKTTDPKGRNAAQSLPPKR   67 (299)
Q Consensus        37 iYT~aP~res-l~Kk~~d~K~~k~~qs~p~Kk   67 (299)
                      .|=|-|.-+. +. -|.+-+|.-...|+|=.=
T Consensus        80 yyLPk~~~e~Yqf-cYv~~~g~V~G~S~pFqf  110 (546)
T PF07888_consen   80 YYLPKDDDEFYQF-CYVDQKGEVRGASTPFQF  110 (546)
T ss_pred             ccCCCCCCCeEEE-EEECCCccEEEecCCccc
Confidence            3556663332 33 344556666666655543

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 [].

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

Probab=91.19  E-value=1.1  Score=43.33  Aligned_cols=128  Identities=29%  Similarity=0.330  Sum_probs=78.2

Q ss_pred             ccchhhhhhhhcHHHH----------HHHHHHHHHHHHHHhhhHHHH-----------HHHHHHHHHHHHHHHHHHHHHH
Q 022306           91 IFSSRALVSEKEIEEL----------VALREQVEDLQRKMFEKDELL-----------KSLESSKSQVNAVHLKLDELKR  149 (299)
Q Consensus        91 ~~~s~~~~~~k~~eEl----------~~LreQVeeLqkKL~EKDelL-----------kSae~~~~em~a~~akvDELr~  149 (299)
                      +..+..-.++|.|.=+          ..|.=||+-|+.+|.|.+|.|           +-++-.+.....++.++|+|+.
T Consensus        82 lk~~l~evEekyrkAMv~naQLDNek~~l~yqvd~Lkd~lee~eE~~~~~~re~~eK~~elEr~K~~~d~L~~e~~~Lre  161 (302)
T PF09738_consen   82 LKDSLAEVEEKYRKAMVSNAQLDNEKSALMYQVDLLKDKLEELEETLAQLQREYREKIRELERQKRAHDSLREELDELRE  161 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555666666655432          344555666666665555543           4566778889999999999999


Q ss_pred             HHHhhHHHHHHHhHHhhH----------------HHHhhhhHHHH--HHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHH
Q 022306          150 LAAEKDSLIKSTQLQLSD----------------AKIKLADKQAA--LEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFM  211 (299)
Q Consensus       150 ~laeKe~likStq~QLsd----------------aki~LadKqAa--LEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm  211 (299)
                      +|.++|.||+--++=|-.                .++-+.-..++  |+..  +-=+=--++-+|-++=..|..+|--|.
T Consensus       162 ~L~~rdeli~khGlVlv~~~~ngd~~~~~~~~~~~~~~~vs~e~a~~L~~a--G~g~LDvRLkKl~~eke~L~~qv~klk  239 (302)
T PF09738_consen  162 QLKQRDELIEKHGLVLVPDATNGDTSDEPNNVGHPKRALVSQEAAQLLESA--GDGSLDVRLKKLADEKEELLEQVRKLK  239 (302)
T ss_pred             HHHHHHHHHHHCCeeeCCCCCCCccccCccccCCCcccccchhhhhhhccc--CCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999755444432                12222211111  1111  000001356677777888889999999


Q ss_pred             HHHhhhhhc
Q 022306          212 QIFEGLIKN  220 (299)
Q Consensus       212 ~~fe~lt~n  220 (299)
                      .+++....+
T Consensus       240 ~qLee~~~~  248 (302)
T PF09738_consen  240 LQLEERQSE  248 (302)
T ss_pred             HHHHHHHhc
Confidence            999765533

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

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.18  E-value=13  Score=35.72  Aligned_cols=100  Identities=28%  Similarity=0.400  Sum_probs=66.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHH----HHh-----------------
Q 022306          104 EELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIK----STQ-----------------  162 (299)
Q Consensus       104 eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~lik----Stq-----------------  162 (299)
                      .||-.|..||++++.|.-++++   -+..+..+|+.++.+|++++..+.++.-+++    ++|                 
T Consensus        52 ~ei~~L~~qi~~~~~k~~~~~~---~i~~~~~eik~l~~eI~~~~~~I~~r~~~l~~raRAmq~nG~~t~Yidvil~SkS  128 (265)
T COG3883          52 NEIESLDNQIEEIQSKIDELQK---EIDQSKAEIKKLQKEIAELKENIVERQELLKKRARAMQVNGTATSYIDVILNSKS  128 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChhHHHHHHHccCc
Confidence            4788899999999998877764   5567778899999999999888888765543    111                 


Q ss_pred             ----------------------HHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhh
Q 022306          163 ----------------------LQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGE  206 (299)
Q Consensus       163 ----------------------~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~e  206 (299)
                                            .++-+-|..|-+||++|++-.-++..-.+..+.++.+|.+-..+
T Consensus       129 fsD~IsRvtAi~~iv~aDk~ile~qk~dk~~Le~kq~~l~~~~e~l~al~~e~e~~~~~L~~qk~e  194 (265)
T COG3883         129 FSDLISRVTAISVIVDADKKILEQQKEDKKSLEEKQAALEDKLETLVALQNELETQLNSLNSQKAE  194 (265)
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                                  12333455666777777766666665555555544444443333

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

Probab=91.02  E-value=3.4  Score=43.19  Aligned_cols=83  Identities=12%  Similarity=0.239  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHH
Q 022306          133 SKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQ  212 (299)
Q Consensus       133 ~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~  212 (299)
                      +..++..+...+++|++.+.++...+..++..+.+.---|++.+|.+.-+-+-+..-...+..|..+.+-++.+|.....
T Consensus       111 ~e~ei~kl~~e~~elr~~~~~~~k~~~~~re~~~~~~~~l~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r~  190 (546)
T KOG0977|consen  111 LEIEITKLREELKELRKKLEKAEKERRGAREKLDDYLSRLSELEAEINTLKRRIKALEDELKRLKAENSRLREELARARK  190 (546)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            35788888999999999999999999999988888888888888877777666666555555555555555555555554


Q ss_pred             HHh
Q 022306          213 IFE  215 (299)
Q Consensus       213 ~fe  215 (299)
                      +++
T Consensus       191 ~ld  193 (546)
T KOG0977|consen  191 QLD  193 (546)
T ss_pred             HHH
Confidence            433

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

Probab=90.86  E-value=15  Score=35.17  Aligned_cols=51  Identities=18%  Similarity=0.368  Sum_probs=20.7

Q ss_pred             HhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHH
Q 022306          164 QLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIF  214 (299)
Q Consensus       164 QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~f  214 (299)
                      +|..++..|++..+.|+....++.....+++.+++++..+..+++.+...+
T Consensus       210 eL~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI  260 (325)
T PF08317_consen  210 ELEALRQELAEQKEEIEAKKKELAELQEELEELEEKIEELEEQKQELLAEI  260 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444444444444444444444444433333

>TIGR01005 eps_transp_fam exopolysaccharide transport protein family

Probab=90.82  E-value=4.4  Score=42.15  Aligned_cols=84  Identities=14%  Similarity=0.186  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHHHHHHHHH-hhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhH---HHHHHHHHhhhhhhHHHH
Q 022306          135 SQVNAVHLKLDELKRLAA-EKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRK---AEKLQEEVESMQGEMSSF  210 (299)
Q Consensus       135 ~em~a~~akvDELr~~la-eKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~K---ve~Lq~dl~~m~~eIssl  210 (299)
                      -+|.++++++++|++++. +...++.+++.++..++......++.+.+++-.+..-+.+   ...|+-+.+..+.-...|
T Consensus       316 P~v~~l~~qi~~l~~~i~~e~~~~~~~~~~~~~~a~~~~~~L~~~l~~~~~~~~~~~~~~~e~~~L~Re~~~~~~~Y~~l  395 (754)
T TIGR01005       316 PRVVAAKSSLADLDAQIRSELQKITKSLLMQADAAQARESQLVSDVNQLKAASAQAGEQQVDLDALQRDAAAKRQLYESY  395 (754)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcHhHHHHHHHHHHHHHHHHHHHHH
Confidence            467777788888887764 4677788888888888888888888888887777655433   335555555555555566


Q ss_pred             HHHHhhhh
Q 022306          211 MQIFEGLI  218 (299)
Q Consensus       211 m~~fe~lt  218 (299)
                      ...++.+.
T Consensus       396 l~r~~e~~  403 (754)
T TIGR01005       396 LTNYRQAA  403 (754)
T ss_pred             HHHHHHHH
Confidence            66665443

The model describes the exopolysaccharide transport protein family in bacteria. The transport protein is part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis. Detailed molecular characterization and gene fusion analysis revealed atleast seven gene products are involved in the overall regulation, which among other things, include exopolysaccharide biosynthesis, property of conferring virulence and exopolysaccharide export.

>PRK10884 SH3 domain-containing protein; Provisional

Probab=90.73  E-value=5.2  Score=36.65  Aligned_cols=84  Identities=18%  Similarity=0.222  Sum_probs=47.8

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEK  181 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEK  181 (299)
                      -++-+-.|+.|+.+|+.+|.+=+.-             .+....+|...+++.+..|..+..+...              
T Consensus        91 ~~~rlp~le~el~~l~~~l~~~~~~-------------~~~~~~~l~~~~~~~~~~~~~L~~~n~~--------------  143 (206)
T PRK10884         91 LRTRVPDLENQVKTLTDKLNNIDNT-------------WNQRTAEMQQKVAQSDSVINGLKEENQK--------------  143 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------
Confidence            5667778888888888887774321             2233344444444444444443333333              


Q ss_pred             HHHHHHHhhhHHHHHHHHHhhhhhhHH--HHHH
Q 022306          182 SQWEAMTVSRKAEKLQEEVESMQGEMS--SFMQ  212 (299)
Q Consensus       182 lewE~~~sn~Kve~Lq~dl~~m~~eIs--slm~  212 (299)
                      |.-|+-+...+++.|+.+++.++..+.  +||+
T Consensus       144 L~~~l~~~~~~~~~l~~~~~~~~~~~~~~wf~~  176 (206)
T PRK10884        144 LKNQLIVAQKKVDAANLQLDDKQRTIIMQWFMY  176 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444455666677777777776553  5654

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

Probab=90.38  E-value=1.5  Score=38.68  Aligned_cols=97  Identities=21%  Similarity=0.292  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHH
Q 022306          105 ELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQW  184 (299)
Q Consensus       105 El~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlew  184 (299)
                      -+..|++.+.+|++          +-..+..+++.+..++.+++..+.+++.-|..++.++.       ..+..+..++-
T Consensus        75 ~~~~l~~ELael~r----------~~~el~~~L~~~~~~l~~l~~~~~~~~~~l~~l~~~~~-------~L~~~~~~l~~  137 (194)
T PF08614_consen   75 KLAKLQEELAELYR----------SKGELAQQLVELNDELQELEKELSEKERRLAELEAELA-------QLEEKIKDLEE  137 (194)
T ss_dssp             -------------------------------------------------HHHHHHHHHHHHH-------HHHHHHHHHHH
T ss_pred             cccccccccccccc----------ccccccccccccccccchhhhhHHHHHHHHHHHHHHHH-------HHHHHHHHHHH
Confidence            34555555555544          34445666677777777777666666665555554443       33334444555


Q ss_pred             HHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          185 EAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       185 E~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      ++...++-++.|+.++.+++-+++.+-..++++.
T Consensus       138 ~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l~  171 (194)
T PF08614_consen  138 ELKEKNKANEILQDELQALQLQLNMLEEKLRKLE  171 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555566666677777777777666666666665

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.

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=90.01  E-value=9.3  Score=45.29  Aligned_cols=110  Identities=24%  Similarity=0.321  Sum_probs=66.6

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHhhHHHH-------HHHhHHhhHHHHhhhhHHH
Q 022306          109 LREQVEDLQRKMFEKDELLKSLESS----KSQVNAVHLKLDELKRLAAEKDSLI-------KSTQLQLSDAKIKLADKQA  177 (299)
Q Consensus       109 LreQVeeLqkKL~EKDelLkSae~~----~~em~a~~akvDELr~~laeKe~li-------kStq~QLsdaki~LadKqA  177 (299)
                      |.+.+.+|+..|.+.++-++++.-.    ..++..+...+.+-++...+-|..+       +-.|.+..+.+..-.+.+.
T Consensus       990 lEe~~~~l~~~l~~~eek~~~l~k~~~kle~~l~~le~~le~e~~~r~e~Ek~~rkle~el~~~~e~~~~~~~~~~el~~ 1069 (1930)
T KOG0161|consen  990 LEERIRELQDDLQAEEEKAKSLNKAKAKLEQQLDDLEVTLEREKRIRMELEKAKRKLEGELKDLQESIEELKKQKEELDN 1069 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            5555555555555555555544433    2444444555554444444444333       4444444555666666667


Q ss_pred             HHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          178 ALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       178 aLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      .|.+.+||+=.-+.|+++++..+..+++.|..|......|.
T Consensus      1070 ~l~kke~El~~l~~k~e~e~~~~~~l~k~i~eL~~~i~el~ 1110 (1930)
T KOG0161|consen 1070 QLKKKESELSQLQSKLEDEQAEVAQLQKQIKELEARIKELE 1110 (1930)
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777777777888888888877777777777666555

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

Probab=90.00  E-value=12  Score=34.42  Aligned_cols=81  Identities=21%  Similarity=0.279  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHHHHHHh-----hHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHH
Q 022306          138 NAVHLKLDELKRLAAE-----KDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQ  212 (299)
Q Consensus       138 ~a~~akvDELr~~lae-----Ke~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~  212 (299)
                      ..+.+.|.++|.++..     |.-+=..-+.++.+.......-..++..+.-|++...+++..|+.++++++....+|-.
T Consensus       165 ~dL~~~L~eiR~~ye~~~~~~~~e~e~~y~~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~  244 (312)
T PF00038_consen  165 SDLSAALREIRAQYEEIAQKNREELEEWYQSKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELESLRAKNASLER  244 (312)
T ss_dssp             --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccchhhhhhHHHHHHHHHhhhhhhhhhhcccccccccccccccccccchhHhHHHHHHhhhhHhhhhhhccccchhhhhh
Confidence            3455566666665532     22333444556666666666666677777778888888888888888888877777777


Q ss_pred             HHhhhh
Q 022306          213 IFEGLI  218 (299)
Q Consensus       213 ~fe~lt  218 (299)
                      .+..+.
T Consensus       245 ~l~~le  250 (312)
T PF00038_consen  245 QLRELE  250 (312)
T ss_dssp             HHHHHH
T ss_pred             hHHHHH
Confidence            666544

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 ....

>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily

Probab=89.96  E-value=9.7  Score=37.44  Aligned_cols=10  Identities=10%  Similarity=0.199  Sum_probs=3.6

Q ss_pred             HHHHHHHHHH
Q 022306          107 VALREQVEDL  116 (299)
Q Consensus       107 ~~LreQVeeL  116 (299)
                      ..++.++++.
T Consensus       171 ~~~~~~L~~a  180 (498)
T TIGR03007       171 KTYEKKLEAA  180 (498)
T ss_pred             HHHHHHHHHH
Confidence            3333333333

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.

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

Probab=89.86  E-value=12  Score=32.25  Aligned_cols=20  Identities=20%  Similarity=0.576  Sum_probs=9.0

Q ss_pred             HHHHHHHhhhhhhHHHHHHH
Q 022306          194 EKLQEEVESMQGEMSSFMQI  213 (299)
Q Consensus       194 e~Lq~dl~~m~~eIsslm~~  213 (299)
                      ..++.+...+...|......
T Consensus       168 ~~~~~~~~~l~~~~~~~~~l  187 (191)
T PF04156_consen  168 ERLQENLQQLEEKIQELQEL  187 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444433

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 [].

>PRK01156 chromosome segregation protein; Provisional

Probab=89.84  E-value=16  Score=38.75  Aligned_cols=13  Identities=31%  Similarity=0.353  Sum_probs=5.3

Q ss_pred             CCCCChHHHHHHH
Q 022306          243 IDDLDDVEMQRME  255 (299)
Q Consensus       243 ~d~~~~~e~~kmE  255 (299)
                      ...++.-....+-
T Consensus       799 ~~~lS~G~~~~~~  811 (895)
T PRK01156        799 IDSLSGGEKTAVA  811 (895)
T ss_pred             cccCCHhHHHHHH
Confidence            3444444433333

>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=89.49  E-value=2.2  Score=37.76  Aligned_cols=96  Identities=22%  Similarity=0.198  Sum_probs=68.6

Q ss_pred             HHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHH-HHHHHHHHHHHHhhhHHHHH
Q 022306          118 RKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQ-AALEKSQWEAMTVSRKAEKL  196 (299)
Q Consensus       118 kKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKq-AaLEKlewE~~~sn~Kve~L  196 (299)
                      ..|.++|.-|.++=..-.+-..++++|..|+.++..+|..|+.+..+|.++...|...- -+-+++     .+..+.++ 
T Consensus         5 ~~L~~~d~~L~~~L~~l~~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~~~~~~~~-----~~~~~~~~-   78 (188)
T PF10018_consen    5 EDLIEADDELSSALEELQEHQENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLPDQADEKL-----KSIPKAEK-   78 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc-----cccccccc-
Confidence            35677777777766667888889999999999999999999999999999999887654 111111     12222221 


Q ss_pred             HHHHhhhhhhHHHHHHHHhhhhhcCCCCC
Q 022306          197 QEEVESMQGEMSSFMQIFEGLIKNDSTVN  225 (299)
Q Consensus       197 q~dl~~m~~eIsslm~~fe~lt~n~S~~~  225 (299)
                            -.+...-|..+=.+|+++.+.+.
T Consensus        79 ------~~v~~~eLL~YA~rISk~t~~p~  101 (188)
T PF10018_consen   79 ------RPVDYEELLSYAHRISKFTSAPP  101 (188)
T ss_pred             ------CCCCHHHHHHHHHHHHHhcCCCC
Confidence                  12235567777789998888743

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

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

Probab=89.40  E-value=13  Score=32.09  Aligned_cols=13  Identities=0%  Similarity=0.026  Sum_probs=5.2

Q ss_pred             HHHHHHHHHHHHh
Q 022306          177 AALEKSQWEAMTV  189 (299)
Q Consensus       177 AaLEKlewE~~~s  189 (299)
                      ..++.+.|++...
T Consensus       158 ~~~~~~~~~~~~~  170 (191)
T PF04156_consen  158 EEVQELRSQLERL  170 (191)
T ss_pred             HHHHHHHHHHHHH
Confidence            3334444444333

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 [].

>PF06818 Fez1: Fez1; InterPro: IPR009638 This family represents the eukaryotic Fez1 protein

Probab=89.24  E-value=4.4  Score=37.54  Aligned_cols=86  Identities=20%  Similarity=0.220  Sum_probs=77.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHH
Q 022306          133 SKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQ  212 (299)
Q Consensus       133 ~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~  212 (299)
                      -.++|+.|.-++-|.+-+++-|+.=|-|+-.||.+++..|..+...+-.++--+-+.+...+..+++|.....|+..|+.
T Consensus         8 k~GEIsLLKqQLke~q~E~~~K~~Eiv~Lr~ql~e~~~~l~~~~~~~~~l~~~~~~K~~ELE~ce~ELqr~~~Ea~lLre   87 (202)
T PF06818_consen    8 KSGEISLLKQQLKESQAEVNQKDSEIVSLRAQLRELRAELRNKESQIQELQDSLRTKQLELEVCENELQRKKNEAELLRE   87 (202)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhHhHHHhHHHHHHHhCHHHHhhh
Confidence            35789999999999999999999999999999999999999999999999988888889999999999999999988877


Q ss_pred             HHhhhh
Q 022306          213 IFEGLI  218 (299)
Q Consensus       213 ~fe~lt  218 (299)
                      .+..+.
T Consensus        88 kl~~le   93 (202)
T PF06818_consen   88 KLGQLE   93 (202)
T ss_pred             hhhhhH
Confidence            766544

Fez1 contains a leucine-zipper region with similarity to the DNA-binding domain of the cAMP-responsive activating-transcription factor 5 []. There is evidence that Fez1 inhibits cancer cell growth through regulation of mitosis, and that its alterations result in abnormal cell growth []. Note that some family members contain more than one copy of this region.; GO: 0005737 cytoplasm, 0016020 membrane

>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily

Probab=88.92  E-value=9.8  Score=37.38  Aligned_cols=60  Identities=17%  Similarity=0.216  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhh
Q 022306          107 VALREQVEDLQRKMFEKDELLKSLESS------------KSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLS  166 (299)
Q Consensus       107 ~~LreQVeeLqkKL~EKDelLkSae~~------------~~em~a~~akvDELr~~laeKe~likStq~QLs  166 (299)
                      .-|..|+..++.+|.+.+..|......            .++++.++.++..++.++++-++.+.+++.+|.
T Consensus       164 ~fl~~ql~~~~~~L~~ae~~l~~f~~~~~~~~~~~~~~~~~~l~~l~~~l~~~~~~l~~~~a~~~~l~~~l~  235 (498)
T TIGR03007       164 RFIDEQIKTYEKKLEAAENRLKAFKQENGGILPDQEGDYYSEISEAQEELEAARLELNEAIAQRDALKRQLG  235 (498)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCcccCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            446778999999999998888876532            255566666666666666666666666665544

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.

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

Probab=88.68  E-value=7.4  Score=33.11  Aligned_cols=48  Identities=21%  Similarity=0.244  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhHHHHH-HHhHHhhHHHHhhhhHHHHH
Q 022306          131 ESSKSQVNAVHLKLDELKRLAAEKDSLIK-STQLQLSDAKIKLADKQAAL  179 (299)
Q Consensus       131 e~~~~em~a~~akvDELr~~laeKe~lik-Stq~QLsdaki~LadKqAaL  179 (299)
                      .+....++.++++|+++++.+.+ +.+.+ -++.+|..+++.-|-.+..|
T Consensus        54 ~s~~qr~~eLqaki~ea~~~le~-eK~ak~~l~~r~~k~~~dka~lel~l  102 (107)
T PF09304_consen   54 ASRNQRIAELQAKIDEARRNLED-EKQAKLELESRLLKAQKDKAILELKL  102 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence            34457788888888888888877 67777 78888888888766655554

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.

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

Probab=88.56  E-value=24  Score=37.33  Aligned_cols=104  Identities=22%  Similarity=0.337  Sum_probs=68.7

Q ss_pred             hcHHHHHHHHHHHHHHHHHHhh----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhH----------Hhh
Q 022306          101 KEIEELVALREQVEDLQRKMFE----KDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQL----------QLS  166 (299)
Q Consensus       101 k~~eEl~~LreQVeeLqkKL~E----KDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~----------QLs  166 (299)
                      .-.+|+.+|+.+++.|..+|-.    +..+=+-....+..+..+..++.++.....|..+|+..+++          |=+
T Consensus        84 ~Lq~E~~~L~kElE~L~~qlqaqv~~ne~Ls~L~~EqEerL~ELE~~le~~~e~~~D~~kLLe~lqsdk~t~SRAlsQN~  163 (617)
T PF15070_consen   84 QLQAEAEHLRKELESLEEQLQAQVENNEQLSRLNQEQEERLAELEEELERLQEQQEDRQKLLEQLQSDKATASRALSQNR  163 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHhHH
Confidence            3456788889889888876543    33332222344678888899999999999999999887773          445


Q ss_pred             HHHHhhhhHHHHHHHHHHHHH--------------HhhhHHHHHHHHHhhhh
Q 022306          167 DAKIKLADKQAALEKSQWEAM--------------TVSRKAEKLQEEVESMQ  204 (299)
Q Consensus       167 daki~LadKqAaLEKlewE~~--------------~sn~Kve~Lq~dl~~m~  204 (299)
                      +-|..|+++|-+.-+|-.+=|              .-.+|..+|+++|+.|.
T Consensus       164 eLK~QL~Elq~~Fv~ltne~~elt~~lq~Eq~~~keL~~kl~~l~~~l~~~~  215 (617)
T PF15070_consen  164 ELKEQLAELQDAFVKLTNENMELTSALQSEQHVKKELQKKLGELQEKLHNLK  215 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567777777776665544422              22345556666555554

>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=88.50  E-value=3.5  Score=40.30  Aligned_cols=66  Identities=30%  Similarity=0.411  Sum_probs=38.9

Q ss_pred             cHHHHHHHHHHHHHHHHHH----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhH
Q 022306          102 EIEELVALREQVEDLQRKM----FEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSD  167 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL----~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsd  167 (299)
                      ..+|+..|..||=+||+++    .|++++..-+..++.-=..+.+.+-+|+..++|=-.++..+|.+|..
T Consensus       232 QQEEIt~LlsqivdlQ~r~k~~~~EnEeL~q~L~~ske~Q~~L~aEL~elqdkY~E~~~mL~EaQEElk~  301 (306)
T PF04849_consen  232 QQEEITSLLSQIVDLQQRCKQLAAENEELQQHLQASKESQRQLQAELQELQDKYAECMAMLHEAQEELKT  301 (306)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666666666666654    35566666665555555555566666666666655555555555543

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 [].

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

Probab=88.45  E-value=19  Score=32.62  Aligned_cols=101  Identities=23%  Similarity=0.347  Sum_probs=74.8

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HhhHHHHHHHhHHhhHHHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLA-----------AEKDSLIKSTQLQLSDAKI  170 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~l-----------aeKe~likStq~QLsdaki  170 (299)
                      =.+-|..++++|++|+++|..=+.--.++..++..+..+..+|..|+.+.           .|||.|-.--..=+++.+.
T Consensus        60 L~epL~~a~~e~~eL~k~L~~y~kdK~~L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~~kf~~~i~evqQ  139 (201)
T PF13851_consen   60 LSEPLKKAEEEVEELRKQLKNYEKDKQSLQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQERDELYRKFESAIQEVQQ  139 (201)
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45778899999999999997655555678888888888888777776543           5666666666666777777


Q ss_pred             hhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHH
Q 022306          171 KLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQ  212 (299)
Q Consensus       171 ~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~  212 (299)
                      +.+-|...||          +|+..|.+.|..-+.++.....
T Consensus       140 k~~~kn~lLE----------kKl~~l~~~lE~keaqL~evl~  171 (201)
T PF13851_consen  140 KTGLKNLLLE----------KKLQALSEQLEKKEAQLNEVLA  171 (201)
T ss_pred             HHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHH
Confidence            7777777776          4777888888877777765543

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

Probab=87.96  E-value=19  Score=40.62  Aligned_cols=107  Identities=20%  Similarity=0.327  Sum_probs=62.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH-----------------------------HHHHHHHHHHHHHHHHHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESSK-----------------------------SQVNAVHLKLDELKRLAA  152 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~-----------------------------~em~a~~akvDELr~~la  152 (299)
                      -++.+..+.+.|..|++++.+..+.|..++++.                             ..+.-.+.+++++...  
T Consensus       226 ~~~~i~~~~e~i~~l~k~i~e~~e~~~~~~~~e~~~~~l~~Lk~k~~W~~V~~~~~ql~~~~~~i~~~qek~~~l~~k--  303 (1074)
T KOG0250|consen  226 AKELIDLKEEEIKNLKKKIKEEEEKLDNLEQLEDLKENLEQLKAKMAWAWVNEVERQLNNQEEEIKKKQEKVDTLQEK--  303 (1074)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--
Confidence            456777888899999999999999999887773                             1111222222222222  


Q ss_pred             hhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHh
Q 022306          153 EKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFE  215 (299)
Q Consensus       153 eKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe  215 (299)
                           |+..+.-..++-.+|-+++|-+..+=-|+-...-.++.+..+|+...-++..|-..+.
T Consensus       304 -----i~~~~~k~~~~r~k~teiea~i~~~~~e~~~~d~Ei~~~r~~~~~~~re~~~~~~~~~  361 (1074)
T KOG0250|consen  304 -----IEEKQGKIEEARQKLTEIEAKIGELKDEVDAQDEEIEEARKDLDDLRREVNDLKEEIR  361 (1074)
T ss_pred             -----HHHHHHHHHHHhhhhhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                 2223333444555555566666666555555555555555665555555555544444

>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=87.02  E-value=6.1  Score=30.77  Aligned_cols=52  Identities=25%  Similarity=0.335  Sum_probs=25.8

Q ss_pred             HHHHHHhhhHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhh
Q 022306          115 DLQRKMFEKDELLKSL----ESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLS  166 (299)
Q Consensus       115 eLqkKL~EKDelLkSa----e~~~~em~a~~akvDELr~~laeKe~likStq~QLs  166 (299)
                      .|.++|.|||+.+.-+    +.+.-.-......|.-||.+..+=+.-|..+...+.
T Consensus         2 sl~~~l~EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~   57 (74)
T PF12329_consen    2 SLEKKLAEKDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLE   57 (74)
T ss_pred             hHHHHHHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3556666666643322    344444444555555555555555544444443333

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.

>PF09763 Sec3_C: Exocyst complex component Sec3; InterPro: IPR019160 The exocyst complex is composed of 8 subunits: Exoc1, Exoc2, Exoc3, Exoc4, Exoc5, Exoc6, Exoc7 and Exoc8

Probab=87.01  E-value=29  Score=36.27  Aligned_cols=110  Identities=17%  Similarity=0.206  Sum_probs=64.6

Q ss_pred             hhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHH---HHHHHHhhhhhcCCCCCCCCCCCCCcccccccCCCCCCC
Q 022306          171 KLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMS---SFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLD  247 (299)
Q Consensus       171 ~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIs---slm~~fe~lt~n~S~~~~~~d~d~~p~~~d~l~~~d~~~  247 (299)
                      .+.++...|....-++..-..-++.++..=.-+|.+..   .|+.-+++|-.         --+++|-.+..|.. ..++
T Consensus        45 e~d~le~~l~~y~~~L~~~~~di~~IE~qn~~Lqvq~~N~k~L~~eL~~Ll~---------~l~i~~~~l~~L~~-~~l~  114 (701)
T PF09763_consen   45 ECDELESWLSLYDVELNSVRDDIEYIESQNNGLQVQSANQKLLLNELENLLD---------TLSIPEEHLEALRN-ASLS  114 (701)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHHHHHH---------hcCCCHHHHHHHhc-CCCC
Confidence            33333334444333333334444444444445555555   34444445542         22245556666666 4454


Q ss_pred             hHH-HHHHHHHHHHHHHHHHHh-----hhcCCHHHHHHHHHHHHhhhhh
Q 022306          248 DVE-MQRMEEAREAYITAVAMA-----KEKQDEESMATAARARLHLQSF  290 (299)
Q Consensus       248 ~~e-~~kmE~aR~aY~aAvaaA-----Kenp~eEsl~~aAeaR~~Lq~f  290 (299)
                      +.+ ++.+|.|=.+--.|+.+-     ...|+-..|.+|.+-|..+..+
T Consensus       115 ~~~~l~~~e~a~~~L~~Al~~i~~~~~~~~~~~~~M~Av~er~~~~~~~  163 (701)
T PF09763_consen  115 SPDGLEKIEEAAEALYKALKAIRPDLEKLDPGLGQMRAVKERREEYEKV  163 (701)
T ss_pred             CcccHHHHHHHHHHHHHHHHhcccccccCCCcHHHHHHHHHHHHHHHHH
Confidence            444 899998888777787772     5778888999999999887643

This entry represents the subunit Exoc1 (Sec3). Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.

>TIGR01005 eps_transp_fam exopolysaccharide transport protein family

Probab=86.85  E-value=19  Score=37.58  Aligned_cols=60  Identities=13%  Similarity=0.195  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHh
Q 022306          106 LVALREQVEDLQRKMFEKDELLKSLESS------------KSQVNAVHLKLDELKRLAAEKDSLIKSTQLQL  165 (299)
Q Consensus       106 l~~LreQVeeLqkKL~EKDelLkSae~~------------~~em~a~~akvDELr~~laeKe~likStq~QL  165 (299)
                      ..-|.+|+.+|+++|.+.|..|..-..-            ..+|+.++.++-..+.+.++.+....+++.+|
T Consensus       196 ~~~L~~ql~~l~~~l~~aE~~l~~fk~~~~l~~~~~~~~~~~~L~~l~~ql~~a~~~~~~a~a~~~~l~~~l  267 (754)
T TIGR01005       196 ADFLAPEIADLSKQSRDAEAEVAAYRAQSDLLMGNNATLATQQLAELNTELSRARANRAAAEGTADSVKKAL  267 (754)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4668899999999999998888766542            15666666666655555555555444444333

The model describes the exopolysaccharide transport protein family in bacteria. The transport protein is part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis. Detailed molecular characterization and gene fusion analysis revealed atleast seven gene products are involved in the overall regulation, which among other things, include exopolysaccharide biosynthesis, property of conferring virulence and exopolysaccharide export.

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=86.65  E-value=17  Score=34.97  Aligned_cols=82  Identities=21%  Similarity=0.235  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHHHHHHh-hHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhH---HHHHHHHHhhhhhhHHHH
Q 022306          135 SQVNAVHLKLDELKRLAAE-KDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRK---AEKLQEEVESMQGEMSSF  210 (299)
Q Consensus       135 ~em~a~~akvDELr~~lae-Ke~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~K---ve~Lq~dl~~m~~eIssl  210 (299)
                      -.|..+.+++++++.++.. -..++.+.+..+..+...+++.++.++.++-++..-+.+   ...|+-|++.-+.--..|
T Consensus       282 P~v~~l~~~i~~l~~~l~~e~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~L~r~~~~~~~~y~~l  361 (444)
T TIGR03017       282 PQYKRAQAEINSLKSQLNAEIKKVTSSVGTNSRILKQREAELREALENQKAKVLELNRQRDEMSVLQRDVENAQRAYDAA  361 (444)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555555432 234455555555555556666666666665555544333   233444454444444455


Q ss_pred             HHHHhh
Q 022306          211 MQIFEG  216 (299)
Q Consensus       211 m~~fe~  216 (299)
                      ...++.
T Consensus       362 l~r~~e  367 (444)
T TIGR03017       362 MQRYTQ  367 (444)
T ss_pred             HHHHHH
Confidence            554443

Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.

>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins

Probab=86.43  E-value=21  Score=31.76  Aligned_cols=93  Identities=14%  Similarity=0.226  Sum_probs=60.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHH-HHHHHHHhhhHHHHHHHHHh
Q 022306          123 KDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEK-SQWEAMTVSRKAEKLQEEVE  201 (299)
Q Consensus       123 KDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEK-lewE~~~sn~Kve~Lq~dl~  201 (299)
                      |+++..-+|....+...+...|++++.++++==.-+-.+...-.-|+..|++--....+ .|-+++.-=.++..+|.+|.
T Consensus        15 K~qIf~I~E~~R~E~~~l~~EL~evk~~v~~~I~evD~Le~~er~aR~rL~eVS~~f~~ysE~dik~AYe~A~~lQ~~L~   94 (159)
T PF05384_consen   15 KEQIFEIAEQARQEYERLRKELEEVKEEVSEVIEEVDKLEKRERQARQRLAEVSRNFDRYSEEDIKEAYEEAHELQVRLA   94 (159)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHHHHHH
Confidence            45555556666666666777777777777666566666666666677777665555544 46666777777777777777


Q ss_pred             hhhhhHHHHHHHHh
Q 022306          202 SMQGEMSSFMQIFE  215 (299)
Q Consensus       202 ~m~~eIsslm~~fe  215 (299)
                      .++.+-..|+.-=+
T Consensus        95 ~~re~E~qLr~rRD  108 (159)
T PF05384_consen   95 MLREREKQLRERRD  108 (159)
T ss_pred             HHHHHHHHHHHHHH
Confidence            77777666665443

The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=85.90  E-value=23  Score=36.31  Aligned_cols=32  Identities=22%  Similarity=0.337  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH
Q 022306          127 LKSLESSKSQVNAVHLKLDELKRLAAEKDSLI  158 (299)
Q Consensus       127 LkSae~~~~em~a~~akvDELr~~laeKe~li  158 (299)
                      +..+..+..++..+.+.++++...+.++..-.
T Consensus       347 ~~~~~~lekeL~~Le~~~~~~~~~i~~~~~~y  378 (569)
T PRK04778        347 LESVRQLEKQLESLEKQYDEITERIAEQEIAY  378 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCH
Confidence            55555555555555555555555555544333

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

Probab=85.85  E-value=32  Score=32.67  Aligned_cols=156  Identities=21%  Similarity=0.234  Sum_probs=81.0

Q ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHH--hhhhHHHHHHHHHHHHHH
Q 022306          111 EQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKI--KLADKQAALEKSQWEAMT  188 (299)
Q Consensus       111 eQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki--~LadKqAaLEKlewE~~~  188 (299)
                      ++.++|++...|++.+.+.++...-++..+..++-.+...+.+=..-++.++..|..++-  ++.+.+-.+..++....+
T Consensus        28 ~~~~~l~k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e~kl~~v~~~~e~~aL~~E~~~ak~r~~~  107 (239)
T COG1579          28 EIRKALKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERINS  107 (239)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHH
Confidence            666777777777777777776666666666666666666655555555555555533221  122222223334444444


Q ss_pred             hhhHHHHHHHHHhhhhhhHHHHHHHHhhhhhcCCCCCCCCCCCCCcccccccCCCCCCChHHHHHHHHHHHHHHHHHHHh
Q 022306          189 VSRKAEKLQEEVESMQGEMSSFMQIFEGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEAREAYITAVAMA  268 (299)
Q Consensus       189 sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt~n~S~~~~~~d~d~~p~~~d~l~~~d~~~~~e~~kmE~aR~aY~aAvaaA  268 (299)
                      -++.+..+.+.+..++.+|..+..-+..+..+-....                   .-.+.++.++.+.+..|..=-.--
T Consensus       108 le~el~~l~~~~~~l~~~i~~l~~~~~~~e~~~~e~~-------------------~~~e~e~~~i~e~~~~~~~~~~~L  168 (239)
T COG1579         108 LEDELAELMEEIEKLEKEIEDLKERLERLEKNLAEAE-------------------ARLEEEVAEIREEGQELSSKREEL  168 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444455555544444444432211111                   112455666666666666555555


Q ss_pred             hhcCCHHHHHHHHHHHH
Q 022306          269 KEKQDEESMATAARARL  285 (299)
Q Consensus       269 Kenp~eEsl~~aAeaR~  285 (299)
                      ++.-+.+.|..=-.-|+
T Consensus       169 ~~~l~~ell~~yeri~~  185 (239)
T COG1579         169 KEKLDPELLSEYERIRK  185 (239)
T ss_pred             HHhcCHHHHHHHHHHHh
Confidence            55555555554444333

>PRK04863 mukB cell division protein MukB; Provisional

Probab=85.81  E-value=31  Score=40.13  Aligned_cols=30  Identities=20%  Similarity=0.323  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022306          103 IEELVALREQVEDLQRKMFEKDELLKSLES  132 (299)
Q Consensus       103 ~eEl~~LreQVeeLqkKL~EKDelLkSae~  132 (299)
                      .||....+.+..+..++|.+++.-|..++.
T Consensus       285 iEEAag~r~rk~eA~kkLe~tE~nL~rI~d  314 (1486)
T PRK04863        285 LEEALELRRELYTSRRQLAAEQYRLVEMAR  314 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345555555555555666665555554443

>cd07623 BAR_SNX1_2 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 1 and 2

Probab=85.78  E-value=27  Score=31.67  Aligned_cols=56  Identities=20%  Similarity=0.263  Sum_probs=47.3

Q ss_pred             HHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhhhc
Q 022306          163 LQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLIKN  220 (299)
Q Consensus       163 ~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt~n  220 (299)
                      ..+..+...|.-|++.++||++.-  ...|++.++.||...+.-......-|+.|+++
T Consensus       123 ~~~q~a~~~l~kkr~~~~Kl~~~~--~~~K~~~~~~ev~~~e~~~~~a~~~fe~is~~  178 (224)
T cd07623         123 QNWQNAQQTLTKKREAKAKLELSG--RTDKLDQAQQEIKEWEAKVDRGQKEFEEISKT  178 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcC--ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345677788899999999998754  35799999999999999999999999999843

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX1, SNX2, and similar proteins. SNX1 and SNX2 are components of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), wh

>PF09325 Vps5: Vps5 C terminal like; InterPro: IPR015404 Vps5 is a sorting nexin that functions in membrane trafficking

Probab=85.72  E-value=24  Score=30.91  Aligned_cols=61  Identities=23%  Similarity=0.290  Sum_probs=55.2

Q ss_pred             HhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhhhcC
Q 022306          161 TQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLIKND  221 (299)
Q Consensus       161 tq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt~n~  221 (299)
                      .+.++..+...|.-|++.++|+.+.-..+..|++.++.++..++.-+..+..-|+.|+++.
T Consensus       133 ~~~~~~~a~~~l~kkk~~~~kl~~~~~~~~~k~~~~~~ei~~~~~~~~~~~~~~~~is~~~  193 (236)
T PF09325_consen  133 KLIEYQNAEKELQKKKAQLEKLKASGKNRQDKVEQAENEIEEAERRVEQAKDEFEEISENI  193 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567788999999999999999998888899999999999999999999999999999653

This is the C-terminal dimerisation domain [].

>KOG0933 consensus Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=85.70  E-value=54  Score=37.33  Aligned_cols=117  Identities=23%  Similarity=0.323  Sum_probs=74.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH---------------------------------HHHHHHHHHHHHHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESSK---------------------------------SQVNAVHLKLDELK  148 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~---------------------------------~em~a~~akvDELr  148 (299)
                      +.+.+...+-|++.-|+.|..=+..|++++...                                 .++..+...|.|++
T Consensus       675 ~l~~l~~~~~~~~~~q~el~~le~eL~~le~~~~kf~~l~~ql~l~~~~l~l~~~r~~~~e~~~~~~~~~~~~e~v~e~~  754 (1174)
T KOG0933|consen  675 QLQKLKQAQKELRAIQKELEALERELKSLEAQSQKFRDLKQQLELKLHELALLEKRLEQNEFHKLLDDLKELLEEVEESE  754 (1174)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHhhHHHHHHHHHHHHHHHH
Confidence            344777777777777777777777777777663                                 66677777888888


Q ss_pred             HHHHhhHHHHHHHhHHhhHHHHh-----------hhhHHHHHHHHHH-------HHHHhhhHHHHHHHHHhhhhhhHHHH
Q 022306          149 RLAAEKDSLIKSTQLQLSDAKIK-----------LADKQAALEKSQW-------EAMTVSRKAEKLQEEVESMQGEMSSF  210 (299)
Q Consensus       149 ~~laeKe~likStq~QLsdaki~-----------LadKqAaLEKlew-------E~~~sn~Kve~Lq~dl~~m~~eIssl  210 (299)
                      .++-+++..++..+...+.-..+           |.|.+.-+..+..       +...+..=++.|+.+.+.|..+|++.
T Consensus       755 ~~Ike~~~~~k~~~~~i~~lE~~~~d~~~~re~rlkdl~keik~~k~~~e~~~~~~ek~~~e~e~l~lE~e~l~~e~~~~  834 (1174)
T KOG0933|consen  755 QQIKEKERALKKCEDKISTLEKKMKDAKANRERRLKDLEKEIKTAKQRAEESSKELEKRENEYERLQLEHEELEKEISSL  834 (1174)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888888877766433222           2222222222222       22222333456777777777777777


Q ss_pred             HHHHhhhh
Q 022306          211 MQIFEGLI  218 (299)
Q Consensus       211 m~~fe~lt  218 (299)
                      ..+++.+.
T Consensus       835 k~~l~~~~  842 (1174)
T KOG0933|consen  835 KQQLEQLE  842 (1174)
T ss_pred             HHHHHHHH
Confidence            77666443

>KOG0976 consensus Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms]

Probab=85.68  E-value=32  Score=38.52  Aligned_cols=56  Identities=14%  Similarity=0.147  Sum_probs=34.3

Q ss_pred             HHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHH--------------HhhhHHHHHHHHHhhhhhhHHHHH
Q 022306          156 SLIKSTQLQLSDAKIKLADKQAALEKSQWEAM--------------TVSRKAEKLQEEVESMQGEMSSFM  211 (299)
Q Consensus       156 ~likStq~QLsdaki~LadKqAaLEKlewE~~--------------~sn~Kve~Lq~dl~~m~~eIsslm  211 (299)
                      .-|...|++|.++++.|.+-.+-|++++-|+-              -++.+..++..++..+-.|++.+-
T Consensus       127 ~ti~~~q~d~ke~etelE~~~srlh~le~eLsAk~~eIf~~~~~L~nk~~~lt~~~~q~~tkl~e~~~en  196 (1265)
T KOG0976|consen  127 DTIQGAQDDKKENEIEIENLNSRLHKLEDELSAKAHDIFMIGEDLHDKNEELNEFNMEFQTKLAEANREK  196 (1265)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhhhhHHHHHHHHHHhhhhhHHhHHHHHHHHHHHHHHHHH
Confidence            34566677777777777777777777776653              344455555555555555555443

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=85.56  E-value=27  Score=33.70  Aligned_cols=104  Identities=12%  Similarity=0.188  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHhhHHHHHH-----------H
Q 022306          106 LVALREQVEDLQRKMFEKDELLKSLESS-------------KSQVNAVHLKLDELKRLAAEKDSLIKS-----------T  161 (299)
Q Consensus       106 l~~LreQVeeLqkKL~EKDelLkSae~~-------------~~em~a~~akvDELr~~laeKe~likS-----------t  161 (299)
                      +.-|.+|+..++++|.+-+..|..-...             ..+++.++.++-..+.++.+-..-...           .
T Consensus       173 ~~fl~~ql~~~~~~l~~ae~~l~~fr~~~~i~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  252 (444)
T TIGR03017       173 ALWFVQQIAALREDLARAQSKLSAYQQEKGIVSSDERLDVERARLNELSAQLVAAQAQVMDASSKEGGSSGKDALPEVIA  252 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccchhhhc
Confidence            4568899999999999999888875543             244555555555555444332221110           0


Q ss_pred             hHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHH
Q 022306          162 QLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSS  209 (299)
Q Consensus       162 q~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIss  209 (299)
                      +..+.+.+..|++.++-+..+.--.-..+-+|-.++..+..++.+|..
T Consensus       253 ~~~i~~l~~~l~~le~~l~~l~~~y~~~hP~v~~l~~~i~~l~~~l~~  300 (444)
T TIGR03017       253 NPIIQNLKTDIARAESKLAELSQRLGPNHPQYKRAQAEINSLKSQLNA  300 (444)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHHHH
Confidence            111223333333333333333222334445555666666665555543

Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.

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

Probab=85.44  E-value=21  Score=29.96  Aligned_cols=105  Identities=22%  Similarity=0.226  Sum_probs=57.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHH
Q 022306          103 IEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKS  182 (299)
Q Consensus       103 ~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKl  182 (299)
                      ..++..|..+...|-...++++.-   ++..++++...+..+..|+.++.+|..-.+......        +-.+.+.+|
T Consensus        33 ~~~~~~l~~~n~~lAe~nL~~~~~---l~~~r~~l~~~~~~~~~L~~~~~~k~~~~~~l~~~~--------s~~~l~~~L  101 (150)
T PF07200_consen   33 QQEREELLAENEELAEQNLSLEPE---LEELRSQLQELYEELKELESEYQEKEQQQDELSSNY--------SPDALLARL  101 (150)
T ss_dssp             HHHHHHHHHHHHHHHHHH----HH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH--------HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcccchH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccC--------CHHHHHHHH
Confidence            344555555555555555555433   333445555666666666666666655444332222        234667778


Q ss_pred             HHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          183 QWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       183 ewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      +-.+.......+.|-+..-.=..++..|-..|....
T Consensus       102 ~~~~~e~eeeSe~lae~fl~g~~d~~~Fl~~f~~~R  137 (150)
T PF07200_consen  102 QAAASEAEEESEELAEEFLDGEIDVDDFLKQFKEKR  137 (150)
T ss_dssp             HHHHHHHHHHHHHHC-S-SSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence            888888888888885554433445667777776544

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.

>PRK10884 SH3 domain-containing protein; Provisional

Probab=85.39  E-value=18  Score=33.13  Aligned_cols=66  Identities=20%  Similarity=0.325  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHHHh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHH
Q 022306          104 EELVALREQVEDLQRKMF-EKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQ  176 (299)
Q Consensus       104 eEl~~LreQVeeLqkKL~-EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKq  176 (299)
                      .|+..|+.+++++....- ++.++=.++..+...++.+.++-++|+.++..       ++.++..++.++.+.+
T Consensus       100 ~el~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~-------~~~~~~~l~~~~~~~~  166 (206)
T PRK10884        100 NQVKTLTDKLNNIDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIV-------AQKKVDAANLQLDDKQ  166 (206)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
Confidence            467777777776665533 23344444555556666666666666665554       4444444444444443

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

Probab=85.37  E-value=35  Score=36.26  Aligned_cols=100  Identities=23%  Similarity=0.302  Sum_probs=74.6

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHH----------------------------HHHHHHHHHHHHHHHHHHHhhHHHHHH
Q 022306          109 LREQVEDLQRKMFEKDELLKSLESS----------------------------KSQVNAVHLKLDELKRLAAEKDSLIKS  160 (299)
Q Consensus       109 LreQVeeLqkKL~EKDelLkSae~~----------------------------~~em~a~~akvDELr~~laeKe~likS  160 (299)
                      +-.+|++|+++..+=.+.+.+++-.                            +..+-..-.+|..|+.++.+|+.-|+.
T Consensus       233 i~~~ie~l~~~n~~l~e~i~e~ek~~~~~eslre~~~~L~~D~nK~~~y~~~~~~k~~~~~~~l~~l~~Eie~kEeE~e~  312 (581)
T KOG0995|consen  233 IANEIEDLKKTNRELEEMINEREKDPGKEESLREKKARLQDDVNKFQAYVSQMKSKKQHMEKKLEMLKSEIEEKEEEIEK  312 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5567778887777766666655543                            133344556788999999999999999


Q ss_pred             HhHHhhHHHHhhh----------hHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHH
Q 022306          161 TQLQLSDAKIKLA----------DKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMS  208 (299)
Q Consensus       161 tq~QLsdaki~La----------dKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIs  208 (299)
                      +|.+-.+-|..+-          .|.+-.++|++++-.-+.+.+.|+.++-...-+|.
T Consensus       313 lq~~~d~Lk~~Ie~Q~iS~~dve~mn~Er~~l~r~l~~i~~~~d~l~k~vw~~~l~~~  370 (581)
T KOG0995|consen  313 LQKENDELKKQIELQGISGEDVERMNLERNKLKRELNKIQSELDRLSKEVWELKLEIE  370 (581)
T ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            9998887765543          46677788888888888888888888877777665

>PF12795 MscS_porin: Mechanosensitive ion channel porin domain

Probab=85.01  E-value=19  Score=32.69  Aligned_cols=87  Identities=17%  Similarity=0.228  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHH---------hhhHHHHHHHH
Q 022306          129 SLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMT---------VSRKAEKLQEE  199 (299)
Q Consensus       129 Sae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~---------sn~Kve~Lq~d  199 (299)
                      +++.+..+++...+.+-++...+++-.+.+.+.+.....+...+.+-...+..+...+..         +.-....|+.+
T Consensus        79 s~~eLeq~l~~~~~~L~~~q~~l~~~~~~l~~~~~~p~~aq~~l~~~~~~l~ei~~~L~~~~~~~~~~l~~a~~~~l~ae  158 (240)
T PF12795_consen   79 SLEELEQRLSQEQAQLQELQEQLQQENSQLIEIQTRPERAQQQLSEARQRLQEIRNQLQNLPPNGESPLSEAQRWLLQAE  158 (240)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchhhHHHHHHHHHH
Confidence            445556777777778888888888888888777777777777777777777777766554         34455566666


Q ss_pred             HhhhhhhHHHHHHHHh
Q 022306          200 VESMQGEMSSFMQIFE  215 (299)
Q Consensus       200 l~~m~~eIsslm~~fe  215 (299)
                      +..+..+|.-+...+.
T Consensus       159 ~~~l~~~~~~le~el~  174 (240)
T PF12795_consen  159 LAALEAQIEMLEQELL  174 (240)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            6666666665554444

>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins

Probab=84.95  E-value=30  Score=38.72  Aligned_cols=102  Identities=20%  Similarity=0.363  Sum_probs=59.9

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHH-H
Q 022306          108 ALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWE-A  186 (299)
Q Consensus       108 ~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE-~  186 (299)
                      .|+++++.+...|.......+.   ...++...+.++++++.++.....-++..+..+...+......+..++..--+ .
T Consensus       604 ~L~~~l~~~~~~l~~~~~~~~~---~e~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  680 (1201)
T PF12128_consen  604 ELRERLEQAEDQLQSAEERQEE---LEKQLKQINKKIEELKREITQAEQELKQAEQDLQRLKNEREQLKQEIEEAKEERK  680 (1201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6777777777777665555433   34455566777777777777777777777666666666555555444442222 2


Q ss_pred             HHhhhHHHHHHHHHhhhhhhHHHHHH
Q 022306          187 MTVSRKAEKLQEEVESMQGEMSSFMQ  212 (299)
Q Consensus       187 ~~sn~Kve~Lq~dl~~m~~eIsslm~  212 (299)
                      ....+++..++.++..+..++..+..
T Consensus       681 ~~~~~~l~~l~~~l~~~~~e~~~~~~  706 (1201)
T PF12128_consen  681 EQIEEQLNELEEELKQLKQELEELLE  706 (1201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555554433

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

Probab=84.83  E-value=22  Score=37.47  Aligned_cols=34  Identities=32%  Similarity=0.449  Sum_probs=26.2

Q ss_pred             hcHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022306          101 KEIEELVALREQVEDLQRKMFEKDELLKSLESSK  134 (299)
Q Consensus       101 k~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~  134 (299)
                      ..-.|+..|++||++|...+.+-+.-++.+....
T Consensus       325 ~~~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~  358 (594)
T PF05667_consen  325 EQEQELEELQEQLDELESQIEELEAEIKMLKSSL  358 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3566889999999999988887777777666554

>KOG0980 consensus Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton]

Probab=84.25  E-value=47  Score=37.19  Aligned_cols=81  Identities=16%  Similarity=0.208  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHH
Q 022306          135 SQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIF  214 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~f  214 (299)
                      -+.......+|++.++..+.+..|.-.+-+.+.+.-|.-+.--+||.++.|....-.++++||..+++....=...-..|
T Consensus       452 kQle~~~~s~~~~~~~~~~L~d~le~~~~~~~~~~~K~e~~~~~le~l~~El~~l~~e~~~lq~~~~~~~qs~~~~~~~l  531 (980)
T KOG0980|consen  452 KQLESAEQSIDDVEEENTNLNDQLEELQRAAGRAETKTESQAKALESLRQELALLLIELEELQRTLSNLAQSHNNQLAQL  531 (980)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            44455555667777777788888888888888888888888889999999999999999999999777655444333333


Q ss_pred             h
Q 022306          215 E  215 (299)
Q Consensus       215 e  215 (299)
                      +
T Consensus       532 ~  532 (980)
T KOG0980|consen  532 E  532 (980)
T ss_pred             H
Confidence            3

>KOG4643 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=84.20  E-value=22  Score=40.25  Aligned_cols=107  Identities=21%  Similarity=0.286  Sum_probs=69.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH---------------------HHHHHHHHHHHHHHH-----hhH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESSKSQV---------------------NAVHLKLDELKRLAA-----EKD  155 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em---------------------~a~~akvDELr~~la-----eKe  155 (299)
                      =..+++.|++.|--|+..|-||-+.|.-+++-..+|                     ..-..++|.++.+..     =|+
T Consensus       175 L~velAdle~kir~LrqElEEK~enll~lr~eLddleae~~klrqe~~e~l~ea~ra~~yrdeldalre~aer~d~~yke  254 (1195)
T KOG4643|consen  175 LEVELADLEKKIRTLRQELEEKFENLLRLRNELDDLEAEISKLRQEIEEFLDEAHRADRYRDELDALREQAERPDTTYKE  254 (1195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHhhhcCCCccch
Confidence            456999999999999999999999998877664222                     222334455554432     145


Q ss_pred             HHHHH--HhHHhhHHH----HhhhhHHHHHHHH------------HHHHHHhhhHHHHHHHHHhhhhhhHH
Q 022306          156 SLIKS--TQLQLSDAK----IKLADKQAALEKS------------QWEAMTVSRKAEKLQEEVESMQGEMS  208 (299)
Q Consensus       156 ~likS--tq~QLsdak----i~LadKqAaLEKl------------ewE~~~sn~Kve~Lq~dl~~m~~eIs  208 (299)
                      ++..|  .-.++-+++    +-|+.|+-+=|+|            |-|+.+=+.|...|+.+.+..|-++.
T Consensus       255 rlmDs~fykdRveelkedN~vLleekeMLeeQLq~lrarse~~tleseiiqlkqkl~dm~~erdtdr~kte  325 (1195)
T KOG4643|consen  255 RLMDSDFYKDRVEELKEDNRVLLEEKEMLEEQLQKLRARSEGATLESEIIQLKQKLDDMRSERDTDRHKTE  325 (1195)
T ss_pred             hhhhhHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence            55555  445554444    4477777665554            45677777788887777665554443

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

Probab=84.09  E-value=19  Score=34.65  Aligned_cols=25  Identities=24%  Similarity=0.323  Sum_probs=17.3

Q ss_pred             HHHHHHhhhhhhHHHHHHHHhhhhh
Q 022306          195 KLQEEVESMQGEMSSFMQIFEGLIK  219 (299)
Q Consensus       195 ~Lq~dl~~m~~eIsslm~~fe~lt~  219 (299)
                      .++.+.+++..++......++.|.+
T Consensus       110 ~~~~e~~sl~~q~~~~~~~L~~L~k  134 (314)
T PF04111_consen  110 EFQEERDSLKNQYEYASNQLDRLRK  134 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4556667777777777777777773

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.

>TIGR01010 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family

Probab=84.00  E-value=40  Score=32.08  Aligned_cols=59  Identities=10%  Similarity=0.130  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHhhHHHHHHHh
Q 022306          104 EELVALREQVEDLQRKMFEKDELLKSLESS------KSQVNAVHLKLDELKRLAAEKDSLIKSTQ  162 (299)
Q Consensus       104 eEl~~LreQVeeLqkKL~EKDelLkSae~~------~~em~a~~akvDELr~~laeKe~likStq  162 (299)
                      +-+.-|++||+.++++|.+-+..|..-...      ..+..+....+.+|+.++++-+.-+..+.
T Consensus       170 ~a~~fl~~ql~~~~~~l~~ae~~l~~fr~~~~~~d~~~~~~~~~~~i~~L~~~l~~~~~~l~~l~  234 (362)
T TIGR01010       170 DTIAFAENEVKEAEQRLNATKAELLKYQIKNKVFDPKAQSSAQLSLISTLEGELIRVQAQLAQLR  234 (362)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345678888999999988888777765553      12333444445555555555544444333

This family contains gamma proteobacterial proteins involved in capsule polysaccharide export.

>KOG4673 consensus Transcription factor TMF, TATA element modulatory factor [Transcription]

Probab=83.88  E-value=33  Score=37.73  Aligned_cols=112  Identities=21%  Similarity=0.261  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHHHHHHH---------HHhhhHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHhhHHHHHHHh
Q 022306          103 IEELVALREQVEDLQR---------KMFEKDELLKSLESS-----------KSQVNAVHLKLDELKRLAAEKDSLIKSTQ  162 (299)
Q Consensus       103 ~eEl~~LreQVeeLqk---------KL~EKDelLkSae~~-----------~~em~a~~akvDELr~~laeKe~likStq  162 (299)
                      ..|--+||-++.-|++         .|.||||++.-+-.-           .+.|.-|.||+-+--..++.+--+|.-++
T Consensus       422 ~kERDalr~e~kslk~ela~~l~~DeLaEkdE~I~~lm~EGEkLSK~ql~qs~iIkKLRAk~ke~etl~~K~ge~i~~L~  501 (961)
T KOG4673|consen  422 TKERDALRREQKSLKKELAAALLKDELAEKDEIINQLMAEGEKLSKKQLAQSAIIKKLRAKIKEAETLEEKKGELITKLQ  501 (961)
T ss_pred             HHhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhhhhHHHHHhhhHHHHHH
Confidence            3466677777764443         566799988765322           37788899999988888888889999999


Q ss_pred             HHhhHHHHhhhhHHHHHHHHHHHHHHh-hhHHHHHHHHHhhhhhhHHHHHHHHh
Q 022306          163 LQLSDAKIKLADKQAALEKSQWEAMTV-SRKAEKLQEEVESMQGEMSSFMQIFE  215 (299)
Q Consensus       163 ~QLsdaki~LadKqAaLEKlewE~~~s-n~Kve~Lq~dl~~m~~eIsslm~~fe  215 (299)
                      +++.--|.-|++|.+ .||+..|.... +--+.+-..+++..+..|..|.....
T Consensus       502 sE~~~lk~il~~Kee-~Ek~~~E~I~k~~ae~~rq~~~~~~sr~~~~~le~~~~  554 (961)
T KOG4673|consen  502 SEENKLKSILRDKEE-TEKLLQETIEKHQAELTRQKDYYSNSRALAAALEAQAL  554 (961)
T ss_pred             HHHHHHHHHhhhHHH-HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence            999999999999975 57777765432 22233333344444444444443333

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=83.68  E-value=25  Score=36.50  Aligned_cols=74  Identities=12%  Similarity=0.149  Sum_probs=40.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQ  176 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKq  176 (299)
                      -+.++..+.+++++|.++|..-+.- ..+.....+++.+..++++++.++.....-|+....++...+..+...+
T Consensus       396 ~~~~~~~~e~el~~l~~~l~~~~~~-e~i~~l~e~l~~l~~~l~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  469 (650)
T TIGR03185       396 LLKELRELEEELAEVDKKISTIPSE-EQIAQLLEELGEAQNELFRSEAEIEELLRQLETLKEAIEALRKTLDEKT  469 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445666666666666666542110 1334444555556666666666666655555555555555555444433

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.

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

Probab=83.62  E-value=31  Score=33.21  Aligned_cols=94  Identities=21%  Similarity=0.308  Sum_probs=58.6

Q ss_pred             hcHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHH
Q 022306          101 KEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALE  180 (299)
Q Consensus       101 k~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLE  180 (299)
                      ...+++..+.++++.|++   |.+++++.++.+..+-..+.+.+..|..+..+.+......-.+....+..+.+.+-.++
T Consensus        40 ~~~~~~~~~~~el~~le~---Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e~~  116 (314)
T PF04111_consen   40 DSEEDIEELEEELEKLEQ---EEEELLQELEELEKEREELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEERD  116 (314)
T ss_dssp             --HH--HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566777777777665   45566666666666777777777777777777666666666666666666666666666


Q ss_pred             HHHHHHHHhhhHHHHHH
Q 022306          181 KSQWEAMTVSRKAEKLQ  197 (299)
Q Consensus       181 KlewE~~~sn~Kve~Lq  197 (299)
                      .++-..-..+...++|+
T Consensus       117 sl~~q~~~~~~~L~~L~  133 (314)
T PF04111_consen  117 SLKNQYEYASNQLDRLR  133 (314)
T ss_dssp             HHHHHHHHHHHHHHCHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            66555555555555555

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.

>PRK04863 mukB cell division protein MukB; Provisional

Probab=83.20  E-value=53  Score=38.29  Aligned_cols=47  Identities=13%  Similarity=0.068  Sum_probs=26.5

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH-------HHHHHHHHHHHHHHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESSKSQ-------VNAVHLKLDELKRLA  151 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~e-------m~a~~akvDELr~~l  151 (299)
                      ..+|...|-|++-..+   .+|.++++.++.....       +..+..++..|++++
T Consensus       277 ~~eERR~liEEAag~r---~rk~eA~kkLe~tE~nL~rI~diL~ELe~rL~kLEkQa  330 (1486)
T PRK04863        277 HANERRVHLEEALELR---RELYTSRRQLAAEQYRLVEMARELAELNEAESDLEQDY  330 (1486)
T ss_pred             CHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5667788888886666   4555555555555433       334444444444443

>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=83.05  E-value=37  Score=31.02  Aligned_cols=107  Identities=12%  Similarity=0.228  Sum_probs=76.3

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHH----HHHHHHH
Q 022306          109 LREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQA----ALEKSQW  184 (299)
Q Consensus       109 LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqA----aLEKlew  184 (299)
                      .+++|+.+.   .||..++...+.+..++..+....+.+.++++.-+.-|.+++.|+.+......+.-.    ++..|+-
T Consensus        40 sQ~~id~~~---~e~~~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~~~~~~~~~l~p~m~~m~~~L~~  116 (251)
T PF11932_consen   40 SQKRIDQWD---DEKQELLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIEQIEETRQELVPLMEQMIDELEQ  116 (251)
T ss_pred             HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444443   367888888888888888888888888888888888888888888888766655554    4444544


Q ss_pred             HHH--------HhhhHHHHHHHHHhhhhhhHH-HHHHHHhhhh
Q 022306          185 EAM--------TVSRKAEKLQEEVESMQGEMS-SFMQIFEGLI  218 (299)
Q Consensus       185 E~~--------~sn~Kve~Lq~dl~~m~~eIs-slm~~fe~lt  218 (299)
                      -|.        .+-..++.|..-|+.-+.-.+ .|+.+|+-+.
T Consensus       117 ~v~~d~Pf~~~eR~~Rl~~L~~~l~~~dv~~~ek~r~vlea~~  159 (251)
T PF11932_consen  117 FVELDLPFLLEERQERLARLRAMLDDADVSLAEKFRRVLEAYQ  159 (251)
T ss_pred             HHhcCCCCChHHHHHHHHHHHHhhhccCCCHHHHHHHHHHHHH
Confidence            222        355677888888877766666 6777777444

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.

>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=82.79  E-value=43  Score=32.95  Aligned_cols=115  Identities=24%  Similarity=0.301  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH-------------------------HHHHHHHHHHHHHHH---HHHhhH
Q 022306          104 EELVALREQVEDLQRKMFEKDELLKSLESSK-------------------------SQVNAVHLKLDELKR---LAAEKD  155 (299)
Q Consensus       104 eEl~~LreQVeeLqkKL~EKDelLkSae~~~-------------------------~em~a~~akvDELr~---~laeKe  155 (299)
                      ++|..-.++|..|+-.|.-||+||+-.-+..                         -.+.+++.|+-.|..   +|..--
T Consensus       104 ~~L~~~~e~v~qLrHeL~~kdeLL~~ys~~~ee~~~~~~~~~~~~~~~~~~~~~~~~~le~Lq~Klk~LEeEN~~LR~Ea  183 (306)
T PF04849_consen  104 EQLGAALEQVEQLRHELSMKDELLQIYSNDDEESEPESSESTPLRRNESSLSSQKCIQLEALQEKLKSLEEENEQLRSEA  183 (306)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCcHhhhcccccCCCccccccccccccccchhHHHHHHHHHHHHHHHHHHHHHH
Confidence            5677788889999999999999987654331                         123344444332221   111111


Q ss_pred             HHHHHHhHHhhHHHHhh--------hhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          156 SLIKSTQLQLSDAKIKL--------ADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       156 ~likStq~QLsdaki~L--------adKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      .-++..-.++.+...+|        ++-..-+.-|.-|+.....=....|+++.++..+|-.+..-+..++
T Consensus       184 ~~L~~et~~~EekEqqLv~dcv~QL~~An~qia~LseELa~k~Ee~~rQQEEIt~LlsqivdlQ~r~k~~~  254 (306)
T PF04849_consen  184 SQLKTETDTYEEKEQQLVLDCVKQLSEANQQIASLSEELARKTEENRRQQEEITSLLSQIVDLQQRCKQLA  254 (306)
T ss_pred             HHhhHHHhhccHHHHHHHHHHHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            11111111122222222        1122223345556666666666777777777777777777777666

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 [].

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=82.63  E-value=38  Score=34.80  Aligned_cols=81  Identities=15%  Similarity=0.224  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhh
Q 022306          137 VNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEG  216 (299)
Q Consensus       137 m~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~  216 (299)
                      +..+..++.++...+.+-..-|..-....+..+..+.+...-|+.++-+-+.-...+..|+.+-...+..+..|...+..
T Consensus       350 ~~~lekeL~~Le~~~~~~~~~i~~~~~~ysel~e~leel~e~leeie~eq~ei~e~l~~Lrk~E~eAr~kL~~~~~~L~~  429 (569)
T PRK04778        350 VRQLEKQLESLEKQYDEITERIAEQEIAYSELQEELEEILKQLEEIEKEQEKLSEMLQGLRKDELEAREKLERYRNKLHE  429 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444444444444343444444444555555555555555555555555555555555544444444444444443


Q ss_pred             h
Q 022306          217 L  217 (299)
Q Consensus       217 l  217 (299)
                      +
T Consensus       430 i  430 (569)
T PRK04778        430 I  430 (569)
T ss_pred             H
Confidence            3

>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=82.27  E-value=16  Score=31.39  Aligned_cols=21  Identities=24%  Similarity=0.450  Sum_probs=11.5

Q ss_pred             hcHHHHHHHHHHHHHHHHHHh
Q 022306          101 KEIEELVALREQVEDLQRKMF  121 (299)
Q Consensus       101 k~~eEl~~LreQVeeLqkKL~  121 (299)
                      .+.+|+..|..+|.+|+.+|.
T Consensus        69 ~s~eel~~ld~ei~~L~~el~   89 (169)
T PF07106_consen   69 PSPEELAELDAEIKELREELA   89 (169)
T ss_pred             CCchhHHHHHHHHHHHHHHHH
Confidence            345556666555555555543

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 [].

>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=82.19  E-value=16  Score=31.95  Aligned_cols=114  Identities=17%  Similarity=0.248  Sum_probs=77.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEK  181 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEK  181 (299)
                      .+..+-.+.++++.|+.+|-+-+.-|+.++.....+..|+++|++|+..+....-        -+++++.=-.+..||+.
T Consensus        18 ~K~~~~~~~~e~~~~k~ql~~~d~~i~~Lk~~~~d~eeLk~~i~~lq~~~~~~~~--------~~e~~l~~~~~~~ai~~   89 (155)
T PF06810_consen   18 PKAKVDKVKEERDNLKTQLKEADKQIKDLKKSAKDNEELKKQIEELQAKNKTAKE--------EYEAKLAQMKKDSAIKS   89 (155)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHH
Confidence            3456667788999999999999999999999888899999999999988864332        22223322334566666


Q ss_pred             HHHHHHHhhhHHHHHHHHHhhhhhh---HHHHHHHHhhhhhcCCC
Q 022306          182 SQWEAMTVSRKAEKLQEEVESMQGE---MSSFMQIFEGLIKNDST  223 (299)
Q Consensus       182 lewE~~~sn~Kve~Lq~dl~~m~~e---Isslm~~fe~lt~n~S~  223 (299)
                      .=..+.-.|.|+-.-.-|++.+.+.   |.-|-.++..|-+++.-
T Consensus        90 al~~akakn~~av~allD~d~l~l~~dg~~Gldeqi~~lkes~~y  134 (155)
T PF06810_consen   90 ALKGAKAKNPKAVKALLDLDKLKLDDDGLKGLDEQIKALKESDPY  134 (155)
T ss_pred             HHHHcCCCCHHHHHHhcCHHHeeeCCCccccHHHHHHHHHhcCch
Confidence            6666666777665555555555322   44566666666655543

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

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=81.77  E-value=55  Score=34.02  Aligned_cols=77  Identities=17%  Similarity=0.233  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHH
Q 022306          105 ELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKS  182 (299)
Q Consensus       105 El~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKl  182 (299)
                      .+..|+.++..++.+|.+-+.-|..+.. ..++..+..+++++.+.+.+-..-+...+.++...+..+...+.-+.++
T Consensus       392 ~~~~~~~~~~~~e~el~~l~~~l~~~~~-~e~i~~l~e~l~~l~~~l~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~  468 (650)
T TIGR03185       392 AKSQLLKELRELEEELAEVDKKISTIPS-EEQIAQLLEELGEAQNELFRSEAEIEELLRQLETLKEAIEALRKTLDEK  468 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555555555444444443321 2466777777777777777776667777666666666666666555554

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.

>KOG0963 consensus Transcription factor/CCAAT displacement protein CDP1 [Transcription]

Probab=81.76  E-value=43  Score=35.93  Aligned_cols=41  Identities=32%  Similarity=0.361  Sum_probs=23.9

Q ss_pred             HHHHHHHhhHHHHH----HHhHHhhHHHHhhhhHHHHHHHHHHHH
Q 022306          146 ELKRLAAEKDSLIK----STQLQLSDAKIKLADKQAALEKSQWEA  186 (299)
Q Consensus       146 ELr~~laeKe~lik----Stq~QLsdaki~LadKqAaLEKlewE~  186 (299)
                      ++-++.++++..++    .+|.|+..+.-+.-.+|.+++..+.+.
T Consensus       175 ~~~q~~~e~e~~L~~~~~~~~~q~~~le~ki~~lq~a~~~t~~el  219 (629)
T KOG0963|consen  175 KLEQEWAEREAGLKDEEQNLQEQLEELEKKISSLQSAIEDTQNEL  219 (629)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Confidence            44455666666554    345666666666666666666655443

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

Probab=81.02  E-value=43  Score=30.39  Aligned_cols=76  Identities=16%  Similarity=0.277  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          143 KLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       143 kvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      ..+.+..++.+++..-...-..+.+-+.++-+.|.....+--+-......+.+|+.+++.+..+|......|+.+.
T Consensus       111 ~~k~le~~~~~~~~~~~~~e~~i~~Le~ki~el~~~~~~~~~~ke~~~~ei~~lks~~~~l~~~~~~~e~~F~~~~  186 (190)
T PF05266_consen  111 ERKKLEKKIEEKEAELKELESEIKELEMKILELQRQAAKLKEKKEAKDKEISRLKSEAEALKEEIENAELEFQSVA  186 (190)
T ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3344444444443333333333333333333333332222222223336678888888888888888888888776

>KOG4438 consensus Centromere-associated protein NUF2 [Cell cycle control, cell division, chromosome partitioning]

Probab=80.98  E-value=53  Score=33.98  Aligned_cols=32  Identities=28%  Similarity=0.416  Sum_probs=23.9

Q ss_pred             hhhcHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 022306           99 SEKEIEELVALREQVEDLQRKMFEKDELLKSL  130 (299)
Q Consensus        99 ~~k~~eEl~~LreQVeeLqkKL~EKDelLkSa  130 (299)
                      ...+-+|+-.|.++|++|+++|.+=--...++
T Consensus       168 ~~~d~ee~kqlEe~ieeL~qsl~kd~~~~~~l  199 (446)
T KOG4438|consen  168 VEEDEEEVKQLEENIEELNQSLLKDFNQQMSL  199 (446)
T ss_pred             ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34577899999999999999988644444444

>cd07627 BAR_Vps5p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p

Probab=80.93  E-value=42  Score=30.16  Aligned_cols=60  Identities=25%  Similarity=0.230  Sum_probs=50.5

Q ss_pred             hHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhhhcC
Q 022306          162 QLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLIKND  221 (299)
Q Consensus       162 q~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt~n~  221 (299)
                      +..+..+...|.-+++.++||.+--.+...|+..++.+|...+..+.....-|+.|+++.
T Consensus       114 ~~~~~~~~~~L~k~~~~~~Kl~~~~~s~~~K~~~~~~ei~~~e~~~~~a~~~~e~is~~~  173 (216)
T cd07627         114 WQYWQSAESELSKKKAQLEKLKRQGKTQQEKLNSLLSELEEAERRASELKKEFEEVSELI  173 (216)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445667888899999999999874344578999999999999999999999999999553

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in

>TIGR01010 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family

Probab=80.76  E-value=48  Score=31.51  Aligned_cols=66  Identities=12%  Similarity=0.279  Sum_probs=30.2

Q ss_pred             cHHHHHHHHHHHHHHHHHHhh-------------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhH
Q 022306          102 EIEELVALREQVEDLQRKMFE-------------KDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSD  167 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~E-------------KDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsd  167 (299)
                      -.+++..++.+++..+.+|.+             -......+..+..++..+..++.+++.-..+.---++.++.|+..
T Consensus       175 l~~ql~~~~~~l~~ae~~l~~fr~~~~~~d~~~~~~~~~~~i~~L~~~l~~~~~~l~~l~~~~~~~~P~v~~l~~~i~~  253 (362)
T TIGR01010       175 AENEVKEAEQRLNATKAELLKYQIKNKVFDPKAQSSAQLSLISTLEGELIRVQAQLAQLRSITPEQNPQVPSLQARIKS  253 (362)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCCcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCchHHHHHHHHH
Confidence            345556666666666555543             111233333444455555555555544444433333333333333

This family contains gamma proteobacterial proteins involved in capsule polysaccharide export.

>KOG0976 consensus Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms]

Probab=80.52  E-value=30  Score=38.69  Aligned_cols=21  Identities=29%  Similarity=0.458  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHhhhHHHHHH
Q 022306          109 LREQVEDLQRKMFEKDELLKS  129 (299)
Q Consensus       109 LreQVeeLqkKL~EKDelLkS  129 (299)
                      ||..-+.|+..|.+|-.+=.|
T Consensus        53 lrserdalhe~lvdkaglneS   73 (1265)
T KOG0976|consen   53 LRSERDALHESLVDKAGLNES   73 (1265)
T ss_pred             HHhhHHHHHHHHHHHhhccch
Confidence            344444555555555444443

>PF08537 NBP1: Fungal Nap binding protein NBP1; InterPro: IPR013743 NBP1 is a nuclear protein which has been shown in Saccharomyces cerevisiae (Bakers yeast) to be essential for the G2/M transition of the cell cycle

Probab=80.42  E-value=8.5  Score=38.07  Aligned_cols=77  Identities=27%  Similarity=0.375  Sum_probs=58.5

Q ss_pred             cHHHHHHHHHHH---HHHHHHHhhh---HHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHhhHHHHHH
Q 022306          102 EIEELVALREQV---EDLQRKMFEK---DELLKSLESS---------------KSQVNAVHLKLDELKRLAAEKDSLIKS  160 (299)
Q Consensus       102 ~~eEl~~LreQV---eeLqkKL~EK---DelLkSae~~---------------~~em~a~~akvDELr~~laeKe~likS  160 (299)
                      .+++-..|++-|   |.+++||.|+   +-+|..+...               -.++-.++.+|++|+++|.+.+..+++
T Consensus       121 ~~e~r~~lk~RI~rSEAFKRKllE~kYD~~mL~qLr~g~~~~~~~~~~~~~~~~D~v~LLqkk~~~l~~~l~~~~~eL~~  200 (323)
T PF08537_consen  121 GREERRLLKDRILRSEAFKRKLLEKKYDKRMLEQLRRGRSKNRHNRPRNPSSNSDRVILLQKKIDELEERLNDLEKELEI  200 (323)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhcCCCCCCcccccCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455656666655   7899999999   3477766544               278999999999999999999999998


Q ss_pred             HhHHhhHHHHhhhhHHHHHHHH
Q 022306          161 TQLQLSDAKIKLADKQAALEKS  182 (299)
Q Consensus       161 tq~QLsdaki~LadKqAaLEKl  182 (299)
                      ++--|.=|+-    |.+.||.|
T Consensus       201 ~~k~L~faqe----kn~Llqsl  218 (323)
T PF08537_consen  201 TKKDLKFAQE----KNALLQSL  218 (323)
T ss_pred             HHHHHHHHHH----HHHHHHHH
Confidence            8888877764    44444443

>PF14988 DUF4515: Domain of unknown function (DUF4515)

Probab=80.35  E-value=47  Score=30.41  Aligned_cols=66  Identities=23%  Similarity=0.258  Sum_probs=47.7

Q ss_pred             HHHHHHHHHH-HHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHH
Q 022306          134 KSQVNAVHLK-LDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSF  210 (299)
Q Consensus       134 ~~em~a~~ak-vDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIssl  210 (299)
                      ..++..-|+. +++|+.++.+++..+..++.+|..    |.+-+.-=++.++|+       ..|+.++..++.+.+.-
T Consensus        38 r~~l~s~y~~q~~~Lq~qLlq~~k~~~~l~~eLq~----l~~~~~~k~~qe~eI-------~~Le~e~~~~~~e~~~~  104 (206)
T PF14988_consen   38 RQELVSRYAKQTSELQDQLLQKEKEQAKLQQELQA----LKEFRRLKEQQEREI-------QTLEEELEKMRAEHAEK  104 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----hHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH
Confidence            4555555554 999999999999999999999865    555555556667665       45777777777776643

>smart00787 Spc7 Spc7 kinetochore protein

Probab=80.21  E-value=60  Score=31.54  Aligned_cols=23  Identities=13%  Similarity=0.261  Sum_probs=11.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhH
Q 022306          102 EIEELVALREQVEDLQRKMFEKD  124 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKD  124 (299)
                      |..-|..-.+.|+++.-+|.+|-
T Consensus       159 D~~~L~~~~~~l~~~~~~l~~~~  181 (312)
T smart00787      159 DYKLLMKELELLNSIKPKLRDRK  181 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444455555555555443

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

---

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	299
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	9e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	8e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 60.6 bits (146), Expect = 2e-10
 Identities = 57/371 (15%), Positives = 107/371 (28%), Gaps = 113/371 (30%)

Query: 3   IATSTKTSSRSSLLSSPSLYDRKASSSFTR--RGSMIYTKTP-SRESLLKKTTDPKGRNA 59
           + +  KT  R      PS+  R       R    + ++ K   SR     K      R A
Sbjct: 94  LMSPIKTEQRQ-----PSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL-----RQA 143

Query: 60  AQSLPPKRKKDN----GDKDLGKN---ANSNQDSD-----SFSIF---SSRALVSEKEIE 104
              L   R   N    G    GK     +            F IF          E  +E
Sbjct: 144 LLEL---RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLE 200

Query: 105 ELVALREQVE-----------DLQRKMFEKDELLKSLESSKSQVNAVHLKLDEL--KRLA 151
            L  L  Q++           +++ ++      L+ L  SK   N + L L  +   +  
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL-LVLLNVQNAKAW 259

Query: 152 AEKD----SLIKSTQLQLSDA-------KIKLADKQAALEKSQWEAM---TVSRKAEKLQ 197
              +     L+ +   Q++D         I L      L   + +++    +  + + L 
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP 319

Query: 198 EEVE-------SMQGEMSSFMQIFEGLIKN-------------DSTVNADDDYDIKPYYS 237
            EV        S+  E    ++       N             +S++N  +  + +  + 
Sbjct: 320 REVLTTNPRRLSIIAES---IRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMF- 375

Query: 238 DYLSDIDDL----DDVEMQRMEEAREAYITAVAMA-----KEKQDEESMATAARARLHLQ 288
                 D L                  +I  + ++       K D   +      +LH  
Sbjct: 376 ------DRLSVFPPSA-----------HIPTILLSLIWFDVIKSDVMVVVN----KLHKY 414

Query: 289 SFVFRNSRRES 299
           S V +  +  +
Sbjct: 415 SLVEKQPKEST 425

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 50.6 bits (120), Expect = 3e-07
 Identities = 37/234 (15%), Positives = 78/234 (33%), Gaps = 60/234 (25%)

Query: 87  DSFSIFSSRALVSEKEIEEL--VALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKL 144
           D  S+F   A +    +  +    ++  V  +  K+ +   + K  + S   + +++L  
Sbjct: 376 DRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYL-- 433

Query: 145 DELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVS-------------- 190
            ELK     + +L +            + D     +    + +                 
Sbjct: 434 -ELKVKLENEYALHR-----------SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHL 481

Query: 191 RKAEKLQEEVESMQGEMSSFMQIF------EGLIKNDST-VNA-----DDDYDIKPYYSD 238
           +  E            M+ F  +F      E  I++DST  NA     +    +K +Y  
Sbjct: 482 KNIE--------HPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLK-FYKP 532

Query: 239 YLSDIDD-----LDDVE--MQRMEEA--REAYITAVAMAKEKQDEESMATAARA 283
           Y+ D D      ++ +   + ++EE      Y   + +A   +DE     A + 
Sbjct: 533 YICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQ 586

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 42.8 bits (101), Expect = 9e-05
 Identities = 28/194 (14%), Positives = 66/194 (34%), Gaps = 18/194 (9%)

Query: 95   RALVSEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEK 154
            R +++++E+++L      VE  ++     +  +  L+           K+DE  +     
Sbjct: 898  RRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQR----------KIDEQNKEYKSL 947

Query: 155  DSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIF 214
               + + ++  S    KL      L  S+        +A+     V S+Q E++   +  
Sbjct: 948  LEKMNNLEITYSTETEKLRSDVERLRMSE-------EEAKNATNRVLSLQEEIAKLRKEL 1000

Query: 215  EGLIKNDSTVNADDDYDIKPYYSDYLSDIDDLDDVEMQRMEEAREAYITAVAMAKEKQDE 274
                    T+    D   K      +S++ + + +     EE             E  ++
Sbjct: 1001 HQTQTEKKTIEEWAD-KYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETMEK 1059

Query: 275  ESMATAARARLHLQ 288
            + +    +  L L 
Sbjct: 1060 KLVEETKQLELDLN 1073

>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-04
 Identities = 27/130 (20%), Positives = 52/130 (40%), Gaps = 10/130 (7%)

Query: 100  EKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIK 159
             K   E   L EQ+ +LQ ++ E    L   E       A   +L++           I+
Sbjct: 1063 RKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALA---RLEDETSQKNNALKKIR 1119

Query: 160  STQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLIK 219
              +  +SD +  L  ++AA  K++       ++   L EE+E+++ E+   +       +
Sbjct: 1120 ELESHISDLQEDLESEKAARNKAE-------KQKRDLSEELEALKTELEDTLDTTATQQE 1172

Query: 220  NDSTVNADDD 229
               +   DDD
Sbjct: 1173 LRGSDYKDDD 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 = 8e-04
 Identities = 20/111 (18%), Positives = 50/111 (45%), Gaps = 1/111 (0%)

Query: 100  EKEIEELVALREQVED-LQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLI 158
             K   +  ++  ++E  L+++   + EL K     + + + +H ++ EL+   AE  + +
Sbjct: 1031 TKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQL 1090

Query: 159  KSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSS 209
               + +L  A  +L D+ +    +  +   +      LQE++ES +   + 
Sbjct: 1091 AKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNK 1141

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	299
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	96.77
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	96.55
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	95.91
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	95.74
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	95.6
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	94.97
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	94.78
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	94.46
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	94.18
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	93.93
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	93.6
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	92.83
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	92.65
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	91.71
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	91.65
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	91.56
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	91.26
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	91.12
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	90.71
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	90.0
4gkw_A	167	Spindle assembly abnormal protein 6; double helix,	89.51
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	89.34
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	89.24
2k48_A	107	Nucleoprotein; viral protein; NMR {Andes virus}	89.12
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	89.1
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	88.74
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	88.56
2e7s_A	135	RAB guanine nucleotide exchange factor SEC2; coile	87.37
3mq9_A	471	Bone marrow stromal antigen 2 fused to maltose-BI	86.96
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	86.84
1gk4_A	84	Vimentin; intermediate filament, dimer, parallel c	86.68
2ic6_A	78	Nucleocapsid protein; hantavirus, bunyaviridae, ss	85.95
4fi5_A	113	Nucleoprotein; structural genomics, niaid, nationa	85.74
1x8y_A	86	Lamin A/C; structural protein, intermediate filame	83.43
3mov_A	95	Lamin-B1; LMNB1, B-type lamins, intermediate filam	83.34
2b9c_A	147	Striated-muscle alpha tropomyosin; alpha-helix, co	82.82
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	82.62
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	82.22
2ic9_A	96	Nucleocapsid protein; hantavirus, bunyaviridae, ss	82.19
2p22_C	192	Protein SRN2; endosome, trafficking complex, VPS23	81.68
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	80.87
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	80.12

>1c1g_A Tropomyosin; contractIle protein; 7.00A {Sus scrofa} SCOP: h.1.5.1 PDB: 2tma_A 2w49_A 2w4u_A

Probab=96.77  E-value=0.16  Score=41.19  Aligned_cols=8  Identities=25%  Similarity=0.322  Sum_probs=2.9

Q ss_pred             HHHHHHHH
Q 022306          109 LREQVEDL  116 (299)
Q Consensus       109 LreQVeeL  116 (299)
                      |.-+++.+
T Consensus        11 l~~~~~~~   18 (284)
T 1c1g_A           11 LKLDKENA   18 (284)
T ss_dssp             HHHHHHHH
T ss_pred             HHHhHHHH
Confidence            33333333

>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=96.55  E-value=0.069  Score=50.78  Aligned_cols=111  Identities=14%  Similarity=0.149  Sum_probs=71.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHhhHHHHHHHhHHhhHH
Q 022306          104 EELVALREQVEDLQRKMFEKDELLKSLESSKSQV---------------NAVHLKLDELKRLAAEKDSLIKSTQLQLSDA  168 (299)
Q Consensus       104 eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em---------------~a~~akvDELr~~laeKe~likStq~QLsda  168 (299)
                      +|+..++..|..|+.++...+..+...+.-..+.               ..+...+..++...+.++..++..+.+..+.
T Consensus       456 ~e~~~~~~~i~~l~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  535 (597)
T 3oja_B          456 AEVNELRAEVQQLTNEQIQQEQLLQGLHAEIDTNLRRYRLPKDGLARSSDNLNKVFTHLKERQAFKLRETQARRTEADAK  535 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCccccccCCHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhhh
Confidence            4666677777777777776666666665554322               4455566666666666666666666666555


Q ss_pred             HHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHH
Q 022306          169 KIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIF  214 (299)
Q Consensus       169 ki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~f  214 (299)
                      +..+...+.-++.+|..+..-.+++..|+.++..+..+|..|+..+
T Consensus       536 ~~~~~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~~  581 (597)
T 3oja_B          536 QKETEDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAKK  581 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             hcchhhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5555555566666777777777777777777777777776665544

>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=95.91  E-value=0.55  Score=38.26  Aligned_cols=108  Identities=15%  Similarity=0.230  Sum_probs=78.4

Q ss_pred             hcHHHHHHHHHHHHHHHHHHhhh----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHH
Q 022306          101 KEIEELVALREQVEDLQRKMFEK----DELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQ  176 (299)
Q Consensus       101 k~~eEl~~LreQVeeLqkKL~EK----DelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKq  176 (299)
                      ..-+|+..+.+++..|+.+|..-    .++=.....+..++|.++.+|..-+-.+++.+-.+..++.+-.+-..+|.+.+
T Consensus        10 ~~e~E~~~~~eel~~lke~l~k~e~~r~ele~~~~~l~~Ek~~L~~qL~~E~~~l~e~EE~~~~L~~~k~eLe~~l~el~   89 (129)
T 2fxo_A           10 EREKEMASMKEEFTRLKEALEKSEARRKELEEKMVSLLQEKNDLQLQVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMN   89 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34578999999999998888633    33444455667999999999999999999999999888888777778888888


Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHH
Q 022306          177 AALEKSQWEAMTVSRKAEKLQEEVESMQGEMS  208 (299)
Q Consensus       177 AaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIs  208 (299)
                      .-|+..+-..-.-..+-.+|+.+++.+..+|.
T Consensus        90 ~rleeeee~~~~L~~~kkkle~e~~~Lk~~le  121 (129)
T 2fxo_A           90 KRLEDEEEMNAELTAKKRKLEDECSELKRDID  121 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88887665544444444445555555544443

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=95.74  E-value=0.059  Score=57.42  Aligned_cols=109  Identities=18%  Similarity=0.228  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHH
Q 022306          106 LVALREQVEDLQRKMFEKDELLKSLE--------SSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQA  177 (299)
Q Consensus       106 l~~LreQVeeLqkKL~EKDelLkSae--------~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqA  177 (299)
                      -..|..+|++||.+|.++++-...+.        ....++..++..+++|+....|+..    +..++.....++++...
T Consensus       923 ~~~LE~kl~eLq~rL~~~e~~n~~L~~~~~~~~~~~~~e~~~L~~~l~~le~~~~e~~~----~~~~v~~L~~e~~~l~~  998 (1080)
T 2dfs_A          923 HIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKN----ATNRVLSLQEEIAKLRK  998 (1080)
T ss_dssp             ----------------------------CHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHH
Confidence            34566666666666665544433222        2245555565556665555444432    12222222223333333


Q ss_pred             HHHHHHHHHHHhhhHH----HHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          178 ALEKSQWEAMTVSRKA----EKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       178 aLEKlewE~~~sn~Kv----e~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      .++++.-|.+.-..+.    ++||+.+++|+.|...|.++++.|.
T Consensus       999 ~~~~~~ke~~~lee~~~~~~~~L~~kv~~L~~e~~~L~qq~~~l~ 1043 (1080)
T 2dfs_A          999 ELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELN 1043 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333332222222222    3445555555555555555555444

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=95.60  E-value=0.21  Score=58.85  Aligned_cols=107  Identities=16%  Similarity=0.215  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhh----
Q 022306          109 LREQVEDLQRKMFEKDELLKSL-----------ESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLA----  173 (299)
Q Consensus       109 LreQVeeLqkKL~EKDelLkSa-----------e~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~La----  173 (299)
                      -.+||++||++|.+|.-.|+..           .....+....++.+++.+.+++++..-|...+   .++...|+    
T Consensus      1932 t~~~V~~l~~~L~~~~~~L~~k~~ea~~~l~~i~~~~~~ae~~k~~v~~~~~~~~~~~~ei~~~k---~~~e~dL~~A~P 2008 (3245)
T 3vkg_A         1932 TEAQVKDLQVSLAQKNRELDVKNEQANQKLKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAVQK---VKAYADLEKAEP 2008 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHCC-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhhcCC
Confidence            4567777777777766555433           33333444444555555555555554444322   23333443    


Q ss_pred             --hHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          174 --DKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       174 --dKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                        =|+++|+++|-++.....+....|+.|..++..|..|...|+..+
T Consensus      2009 a~Pkr~~l~~ae~~l~~~~~~L~~~~~~L~~le~~l~~L~~~~~~~~ 2055 (3245)
T 3vkg_A         2009 TGPLREEVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLI 2055 (3245)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              366777777777777777777778888877777777777777554

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=94.97  E-value=1.6  Score=38.69  Aligned_cols=116  Identities=12%  Similarity=0.205  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHh
Q 022306          105 ELVALREQVEDLQRKMFEKDELLKSLESSK-------------SQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIK  171 (299)
Q Consensus       105 El~~LreQVeeLqkKL~EKDelLkSae~~~-------------~em~a~~akvDELr~~laeKe~likStq~QLsdaki~  171 (299)
                      .+..++.+++++++.+...+.-+..+...+             -++.++...|+.+++....-+.-|.-..-++...+..
T Consensus        47 ~~~~~~~~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l~~v~~~kE~~aL~kEie~~~~~i~~lE~eile~~e~ie~~~~~  126 (256)
T 3na7_A           47 AILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMSEIKSERELRSLNIEEDIAKERSNQANREIENLQNEIKRKSEK  126 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444445555555544444444444332             3344444455544444444443333333333333333


Q ss_pred             hhhHHHHHHHHHHHHH----HhhhHHHHHHHHHh-------hhhhhHH-HHHHHHhhhhhc
Q 022306          172 LADKQAALEKSQWEAM----TVSRKAEKLQEEVE-------SMQGEMS-SFMQIFEGLIKN  220 (299)
Q Consensus       172 LadKqAaLEKlewE~~----~sn~Kve~Lq~dl~-------~m~~eIs-slm~~fe~lt~n  220 (299)
                      +++.++.++.++-++.    .....+..++.++.       .+...|. .|...|+.|.++
T Consensus       127 l~~~~~~l~~~~~~l~~~~~~~~~~~~e~~~e~~~l~~~r~~l~~~i~~~lL~~Yerir~~  187 (256)
T 3na7_A          127 QEDLKKEMLELEKLALELESLVENEVKNIKETQQIIFKKKEDLVEKTEPKIYSFYERIRRW  187 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            3333333333322221    11222333333333       3333333 677788888853

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=94.78  E-value=0.69  Score=37.50  Aligned_cols=54  Identities=28%  Similarity=0.463  Sum_probs=38.8

Q ss_pred             HHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhh
Q 022306          163 LQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEG  216 (299)
Q Consensus       163 ~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~  216 (299)
                      .+|.+++..++++.+.|.++.++...-..--..|=+==-.++.||.+.+.+++|
T Consensus        75 ~~l~~~q~~i~~lE~eL~~~r~e~~~ql~EYq~LlnvKl~Ld~EIatYRkLLEg  128 (129)
T 3tnu_B           75 LALKDARNKLAELEEALQKAKQDMARLLREYQELMNTKLALDVEIATYRKLLEG  128 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHCc
Confidence            467777777888888888888777665555555544444688999999888764

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=94.46  E-value=0.37  Score=39.29  Aligned_cols=55  Identities=15%  Similarity=0.283  Sum_probs=39.2

Q ss_pred             hHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhh
Q 022306          162 QLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEG  216 (299)
Q Consensus       162 q~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~  216 (299)
                      ..+|.+++..++++.+.|.++.++...-..--..|=+==-.++.||++.+.+|++
T Consensus        76 ~~~l~~~q~~i~~lE~eL~~~r~em~~ql~EYq~Ll~vKl~Ld~EIatYRkLLEG  130 (131)
T 3tnu_A           76 CMQLAQIQEMIGSVEEQLAQLRCEMEQQNQEYKILLDVKTRLEQEIATYRRLLEG  130 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHCc
Confidence            3466777777788888888887777665555555544444688999999988874

>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

Probab=94.18  E-value=0.071  Score=56.59  Aligned_cols=17  Identities=18%  Similarity=0.259  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHHHHHHh
Q 022306          105 ELVALREQVEDLQRKMF  121 (299)
Q Consensus       105 El~~LreQVeeLqkKL~  121 (299)
                      |+..|.+++++|+.+|.
T Consensus       858 El~~L~~eL~el~~~L~  874 (1184)
T 1i84_S          858 EMQAKDEELQRTKERQQ  874 (1184)
T ss_dssp             HCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            44444444444444433

>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

Probab=93.93  E-value=0.29  Score=51.98  Aligned_cols=14  Identities=21%  Similarity=0.302  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHHHHH
Q 022306          105 ELVALREQVEDLQR  118 (299)
Q Consensus       105 El~~LreQVeeLqk  118 (299)
                      ++..|+++++.++.
T Consensus       865 eL~el~~~L~~le~  878 (1184)
T 1i84_S          865 ELQRTKERQQKAEA  878 (1184)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333333333333

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=93.60  E-value=2.8  Score=36.66  Aligned_cols=81  Identities=15%  Similarity=0.185  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhh----hhHHHH
Q 022306          135 SQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQ----GEMSSF  210 (299)
Q Consensus       135 ~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~----~eIssl  210 (299)
                      .++..+++.+++=|+...--.-+|.-+|..+...+..|......+.+++-|-..=..|+..|+-+-++++    |++-++
T Consensus        69 ke~~~LQa~L~qEr~~r~q~se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r~L~Ekl~~lEKe~a~~eid~~~eLKal  148 (168)
T 3o0z_A           69 KDYYQLQAILEAERRDRGHDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEAQDMLNHSEKEKNNLEIDLNYKLKSL  148 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            5555666666666655566666666677777777777777777777777777777777777777777777    555566


Q ss_pred             HHHHh
Q 022306          211 MQIFE  215 (299)
Q Consensus       211 m~~fe  215 (299)
                      +.-++
T Consensus       149 Q~~~e  153 (168)
T 3o0z_A          149 QQRLE  153 (168)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65554

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=92.83  E-value=1.6  Score=46.56  Aligned_cols=46  Identities=20%  Similarity=0.205  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022306          103 IEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELK  148 (299)
Q Consensus       103 ~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr  148 (299)
                      -.|+..|+.++++|+....|+..+-..+.++..++..+..++..+.
T Consensus       959 ~~e~~~L~~~l~~le~~~~e~~~~~~~v~~L~~e~~~l~~~~~~~~ 1004 (1080)
T 2dfs_A          959 STETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQ 1004 (1080)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555555555555544444334444444444443333333

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=92.65  E-value=0.25  Score=40.38  Aligned_cols=54  Identities=20%  Similarity=0.379  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHH
Q 022306          106 LVALREQVEDLQRKMFEKDELL-----------KSLESSKSQVNAVHLKLDELKRLAAEKDSLIK  159 (299)
Q Consensus       106 l~~LreQVeeLqkKL~EKDelL-----------kSae~~~~em~a~~akvDELr~~laeKe~lik  159 (299)
                      -.+|.=||+-|+-+|-|.++.+           +-++.++-....++.++++|+.+|.++|.||.
T Consensus        25 Ksal~YqVdlLKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~~lk~~L~qRD~LI~   89 (103)
T 4h22_A           25 KTNFMYQVDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEVKEALKQREEMLE   89 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSCC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445556666666665555544           44666678889999999999999999999985

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=91.71  E-value=1.7  Score=34.22  Aligned_cols=64  Identities=17%  Similarity=0.249  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHH
Q 022306          124 DELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAM  187 (299)
Q Consensus       124 DelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~  187 (299)
                      |+-.+-+|.++.+||.+.-+|.||-.+-.-=|.=++||..+|+--+..|+.|.|.++.|+-++.
T Consensus        15 ee~~~~~E~L~qEi~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l~   78 (81)
T 3qh9_A           15 EEKQRKAEELLQELRHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQLS   78 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHHh
Confidence            4455677788888999998888888777777777888888888888888888888888776653

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=91.65  E-value=6.7  Score=34.63  Aligned_cols=25  Identities=8%  Similarity=0.097  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHH
Q 022306          136 QVNAVHLKLDELKRLAAEKDSLIKS  160 (299)
Q Consensus       136 em~a~~akvDELr~~laeKe~likS  160 (299)
                      ++..++..++.+++++...+.-|..
T Consensus        47 ~~~~~~~~l~d~~~~~~~~e~~i~~   71 (256)
T 3na7_A           47 AILNLEEEKLALKLQVSKNEQTLQD   71 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333344444433333333333

>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=91.56  E-value=0.54  Score=36.22  Aligned_cols=45  Identities=33%  Similarity=0.336  Sum_probs=31.7

Q ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhH
Q 022306          113 VEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSD  167 (299)
Q Consensus       113 VeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsd  167 (299)
                      |-+||.-|-+|++=          +..-...|++|.++|.+||..|+-+|++|..
T Consensus        21 i~eLq~~L~~K~eE----------Lr~kd~~I~eLEk~L~ekd~eI~~LqseLDK   65 (72)
T 3nmd_A           21 LRDLQYALQEKIEE----------LRQRDALIDELELELDQKDELIQMLQNELDK   65 (72)
T ss_dssp             HHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55666666666653          3444556778888888888888888888864

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=91.26  E-value=2.3  Score=35.05  Aligned_cols=37  Identities=27%  Similarity=0.425  Sum_probs=20.7

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH
Q 022306          112 QVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLI  158 (299)
Q Consensus       112 QVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~li  158 (299)
                      +|++|+.+|-.-+++|..          -+..+|+|+..++.++.-+
T Consensus        25 ei~~L~~~L~~AEeaL~~----------Kq~~idelk~ei~q~~~~l   61 (110)
T 2v4h_A           25 QLEDLRQQLQQAEEALVA----------KQELIDKLKEEAEQHKIVM   61 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHH
Confidence            555666666655555544          3445566666666655533

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=91.12  E-value=2.5  Score=34.20  Aligned_cols=101  Identities=14%  Similarity=0.252  Sum_probs=37.0

Q ss_pred             hcHHHHHH-HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHH
Q 022306          101 KEIEELVA-LREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAAL  179 (299)
Q Consensus       101 k~~eEl~~-LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaL  179 (299)
                      +++.|+-. -+.++++|+...---.+.|++   .+.+++.++-.|..|.-++..=.+...++..+|.+++.         
T Consensus         4 knr~eaE~~y~~K~eel~~~~~~~~~~l~~---~k~Ei~elrr~iq~L~~el~~l~~~~~~LE~~l~e~e~---------   71 (129)
T 3tnu_B            4 RSRTEAESWYQTKYEELQQTAGRHGDDLRN---TKHEISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQ---------   71 (129)
T ss_dssp             ---------------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH---------
Confidence            44444433 356677777655444444433   34444444444444444443333333344444444332         


Q ss_pred             HHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHH
Q 022306          180 EKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIF  214 (299)
Q Consensus       180 EKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~f  214 (299)
                       ..+.++..-+.++..|+.+|..++.++.....-+
T Consensus        72 -~~~~~l~~~q~~i~~lE~eL~~~r~e~~~ql~EY  105 (129)
T 3tnu_B           72 -RGELALKDARNKLAELEEALQKAKQDMARLLREY  105 (129)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence             2334555566677777777777777776544333

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=90.71  E-value=6  Score=37.54  Aligned_cols=112  Identities=13%  Similarity=0.093  Sum_probs=68.2

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------------hhHHHHHHHhHHhh
Q 022306          105 ELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAA------------------EKDSLIKSTQLQLS  166 (299)
Q Consensus       105 El~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~la------------------eKe~likStq~QLs  166 (299)
                      ...+|+++++++..++..=.+-   .......++....++++.+..+.                  .=....+....++.
T Consensus       450 ~~e~l~~e~~~~~~~i~~l~~~---~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  526 (597)
T 3oja_B          450 GNEQLEAEVNELRAEVQQLTNE---QIQQEQLLQGLHAEIDTNLRRYRLPKDGLARSSDNLNKVFTHLKERQAFKLRETQ  526 (597)
T ss_dssp             ----CCHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHTTCCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhhhhhhhcCccccccCCHHHHHHHHHHHHHhhhhhhHHHHH
Confidence            4556777877777655433332   33344556666666666655544                  11122223333444


Q ss_pred             HHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhhh
Q 022306          167 DAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLIK  219 (299)
Q Consensus       167 daki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt~  219 (299)
                      ..+....+++..+++++.|+..-.++.+..+..+..+..|+...+..+..+-+
T Consensus       527 ~~~~~~~~~~~~~~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~  579 (597)
T 3oja_B          527 ARRTEADAKQKETEDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEA  579 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhhhcchhhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            55555666777788888888888888888888888888888877666665553

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=90.00  E-value=3  Score=34.78  Aligned_cols=99  Identities=15%  Similarity=0.085  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHHHHHHHHhhh--HH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhh
Q 022306          104 EELVALREQVEDLQRKMFEK--DE-------LLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLAD  174 (299)
Q Consensus       104 eEl~~LreQVeeLqkKL~EK--De-------lLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~Lad  174 (299)
                      +-|..+=.-|++-=+.+...  -.       +.=.|=+.-.++-.++..+++|..++.+++.=|.++-.+|-.+++++..
T Consensus        28 e~L~~vA~~vd~km~ei~~~~~~~~l~~~r~aVLaALNiadEl~k~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~  107 (138)
T 3hnw_A           28 EYLQRVASYINNKITEFNKEESYRRMSAELRTDMMYLNIADDYFKAKKMADSLSLDIENKDKEIYDLKHELIAAQIKAES  107 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45555555555555555533  22       2222333347777778888888888888888888888888888888877


Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHhh
Q 022306          175 KQAALEKSQWEAMTVSRKAEKLQEEVES  202 (299)
Q Consensus       175 KqAaLEKlewE~~~sn~Kve~Lq~dl~~  202 (299)
                      -...+++|+.++-.-..++-+|+.++..
T Consensus       108 ~~~e~~~l~~~~~~l~~~~~~le~~~~~  135 (138)
T 3hnw_A          108 SAKEIKELKSEINKYQKNIVKLETELND  135 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            7777777777777766666666666543

>4gkw_A Spindle assembly abnormal protein 6; double helix, SAS-5, centriole, structural protein; 3.30A {Caenorhabditis elegans}

Probab=89.51  E-value=5.3  Score=34.51  Aligned_cols=60  Identities=32%  Similarity=0.355  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHh
Q 022306          103 IEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQ  162 (299)
Q Consensus       103 ~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq  162 (299)
                      -.||..||...+-+|+++---|.+|+--.+-.++-+.=--|+-||.--|-|||+.+.|+-
T Consensus        59 QKEi~~Lrae~~~~QRn~~K~~~~Lkrn~~qQnQQSlDiRKLrELEADLKEKDsMVe~LT  118 (167)
T 4gkw_A           59 QKEIGKLRAELGTAQRNLEKADQLLKRNSQQQNQQSLDMRKLGELEADLKEKDSMVESLT  118 (167)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHhhhHHHhHhhhhHHHHHHHHhHHhhhhHHHHHHH
Confidence            358899999999999999888999987777777777777888999999999999998854

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=89.34  E-value=4.7  Score=33.59  Aligned_cols=64  Identities=17%  Similarity=0.212  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHH
Q 022306          103 IEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAK  169 (299)
Q Consensus       103 ~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdak  169 (299)
                      -+|+..++++++.|...+-+++   +.+..++.++..++-+++++++++.+-..=+..+|-++....
T Consensus        67 adEl~k~~~~~~~L~~~l~~~~---kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le  130 (138)
T 3hnw_A           67 ADDYFKAKKMADSLSLDIENKD---KEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLE  130 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4589999999999998887764   555667778888888888888888776666666666655443

>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=89.24  E-value=3.9  Score=30.78  Aligned_cols=75  Identities=13%  Similarity=0.125  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhh
Q 022306          138 NAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGL  217 (299)
Q Consensus       138 ~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~l  217 (299)
                      .++..||-.|+.+.       ..++..+..+...|-+.....++++-|+..-++|..-|++||+..+..+......|+..
T Consensus         2 ~~ikkKm~~lk~e~-------d~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~ee~l~~a~~kLeea   74 (81)
T 1ic2_A            2 DAIKKKMQMLKLDK-------ENALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESLKDAQEKLELA   74 (81)
T ss_dssp             CHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555555443       23455666667777777778899999999999999999999999999999888888866


Q ss_pred             hh
Q 022306          218 IK  219 (299)
Q Consensus       218 t~  219 (299)
                      .+
T Consensus        75 ek   76 (81)
T 1ic2_A           75 DK   76 (81)
T ss_dssp             GG
T ss_pred             HH
Confidence            54

>2k48_A Nucleoprotein; viral protein; NMR {Andes virus}

Probab=89.12  E-value=1.1  Score=36.81  Aligned_cols=50  Identities=24%  Similarity=0.379  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022306          105 ELVALREQVEDLQRKMFEKDEL---------LKSLESSKSQVNAVHLKLDELKRLAAEK  154 (299)
Q Consensus       105 El~~LreQVeeLqkKL~EKDel---------LkSae~~~~em~a~~akvDELr~~laeK  154 (299)
                      |+-...-|+---++||-+=...         ..++.+....+++++.||.+|++++|+.
T Consensus        43 Ei~~~E~QL~iArQKLkdAe~~~E~DPDevNK~tl~~R~~~Vsalq~KiaeLKrqLAd~  101 (107)
T 2k48_A           43 NITAHEQQLVTARQKLKDAEKAVEVDPDDVNKSTLQNRRAAVSTLETKLGELKRQLADL  101 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555566666666543322         3455566788888889999998888875

>3u1c_A Tropomyosin alpha-1 chain; anti-parallel coiled coil, contractIle protein; 1.80A {Gallus gallus} PDB: 3u1a_A

Probab=89.10  E-value=7  Score=30.73  Aligned_cols=38  Identities=16%  Similarity=0.191  Sum_probs=23.6

Q ss_pred             HhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHH
Q 022306          161 TQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQE  198 (299)
Q Consensus       161 tq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~  198 (299)
                      ++.+|.+++.+|-+..-.+...|.|+..-|+|+--|++
T Consensus        63 ~ee~L~ea~~kLee~ek~~~~aE~ev~~L~RriqllEE  100 (101)
T 3u1c_A           63 VLEELHKSEDSLLFAEENAAKAESEVASLNRRIQLVEE  100 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            45566666666666666666666666666666655543

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=88.74  E-value=12  Score=32.78  Aligned_cols=101  Identities=21%  Similarity=0.267  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHH
Q 022306          106 LVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWE  185 (299)
Q Consensus       106 l~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE  185 (299)
                      +..|+-|+++++.||.-=-+.-.-+.-..+++....+.++..-++|.+|=..+..   +.-.-...++..|+.|+.=-+.
T Consensus         8 i~~LekQL~E~n~kLk~EsE~~~rlkK~~tEl~k~~~~~E~~~rELq~~~~~L~~---~k~~Leke~~~LQa~L~qEr~~   84 (168)
T 3o0z_A            8 LSQLQKQLEEANDLLRTESDTAVRLRKSHTEMSKSISQLESLNRELQERNRILEN---SKSQTDKDYYQLQAILEAERRD   84 (168)
T ss_dssp             --CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
Confidence            3556667777776664333333333333456666666666666666665443333   3333345566667776654444


Q ss_pred             HHHhhhHHHHHHHHHhhhhhhHHH
Q 022306          186 AMTVSRKAEKLQEEVESMQGEMSS  209 (299)
Q Consensus       186 ~~~sn~Kve~Lq~dl~~m~~eIss  209 (299)
                      --..+.-+.+||+.+.+++.|+..
T Consensus        85 r~q~se~~~elq~ri~~L~~El~~  108 (168)
T 3o0z_A           85 RGHDSEMIGDLQARITSLQEEVKH  108 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444334444444444444443

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=88.56  E-value=6.1  Score=47.06  Aligned_cols=117  Identities=14%  Similarity=0.246  Sum_probs=71.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHH----HH-------HHHHHHHHHHHHHHHHHHH------------------------
Q 022306          102 EIEELVALREQVEDLQRKMFEKDE----LL-------KSLESSKSQVNAVHLKLDE------------------------  146 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDe----lL-------kSae~~~~em~a~~akvDE------------------------  146 (299)
                      -.+.+..|++++.++|.+|.+|..    +|       ..|+.-+..+.+..+++.+                        
T Consensus      1932 t~~~V~~l~~~L~~~~~~L~~k~~ea~~~l~~i~~~~~~ae~~k~~v~~~~~~~~~~~~ei~~~k~~~e~dL~~A~Pa~P 2011 (3245)
T 3vkg_A         1932 TEAQVKDLQVSLAQKNRELDVKNEQANQKLKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAVQKVKAYADLEKAEPTGP 2011 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-------C
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCh
Confidence            456777888888888888777632    21       2333333333333333222                        


Q ss_pred             HHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          147 LKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       147 Lr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      +|..|++=+.-+..++.+|..++.+|++.++.|++|+-+.-....+.+.|+.+++..+.-+..=..++.+|+
T Consensus      2012 kr~~l~~ae~~l~~~~~~L~~~~~~L~~le~~l~~L~~~~~~~~~ek~~L~~e~~~~~~kl~rA~~Li~gL~ 2083 (3245)
T 3vkg_A         2012 LREEVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSIALLDNLN 2083 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            233444444455566667777777777777777777777766677777777777777766665555555555

>2e7s_A RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 3.00A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=87.37  E-value=1.3  Score=37.54  Aligned_cols=34  Identities=29%  Similarity=0.366  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhh
Q 022306          139 AVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKL  172 (299)
Q Consensus       139 a~~akvDELr~~laeKe~likStq~QLsdaki~L  172 (299)
                      .+..+++.|+.++.||+.+|.+.|.||.+-|.-+
T Consensus       100 ~~e~r~~~L~~ql~e~e~ll~~lq~QL~~LK~v~  133 (135)
T 2e7s_A          100 AIEILNKRLTEQLREKDMLLDTLTLQLKNLKKVM  133 (135)
T ss_dssp             HHHHHHHHHHHTTTHHHHCC--------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3577888899999999999999999988877543

>3mq9_A Bone marrow stromal antigen 2 fused to maltose-BI periplasmic protein; HIV, antiviral protein; 2.80A {Escherichia coli}

Probab=86.96  E-value=19  Score=33.37  Aligned_cols=34  Identities=18%  Similarity=0.231  Sum_probs=17.9

Q ss_pred             HHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhh
Q 022306          183 QWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEG  216 (299)
Q Consensus       183 ewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~  216 (299)
                      +-++-.-.+|+++|++++..+..+|.-+...++.
T Consensus       435 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  468 (471)
T 3mq9_A          435 DAEKAQGQKKVEELEGEITTLNHKLQDASAEVER  468 (471)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444456666666666655555555554443

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=86.84  E-value=4.4  Score=35.02  Aligned_cols=60  Identities=18%  Similarity=0.165  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHHH
Q 022306          127 LKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWEA  186 (299)
Q Consensus       127 LkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE~  186 (299)
                      +..+..+..+...+..+|..|...+.+|..++..+|.++.--++.+.-.+..+.+||-|-
T Consensus        67 ~~~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE~kl~kLq~EN  126 (152)
T 3a7p_A           67 LNTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKLSDLKKEH  126 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            557888889999999999999999999999999999999999999988888888888764

>1gk4_A Vimentin; intermediate filament, dimer, parallel coiled coil, heptad repeat, stutter; 2.3A {Homo sapiens} SCOP: h.1.20.1

Probab=86.68  E-value=8.8  Score=29.14  Aligned_cols=54  Identities=13%  Similarity=0.224  Sum_probs=35.9

Q ss_pred             HHhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhh
Q 022306          163 LQLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEG  216 (299)
Q Consensus       163 ~QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~  216 (299)
                      .++.+.+..++...+.|.++..+.-.-..--..|=+==-.++.||++.+.++++
T Consensus        26 ~~~~~~q~~i~~lE~eL~~~r~e~~~q~~EYq~LlnvK~~Ld~EIatYRkLLEG   79 (84)
T 1gk4_A           26 VEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEG   79 (84)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHcC
Confidence            356667777777777777777666544444333333334578999999999885

>2ic6_A Nucleocapsid protein; hantavirus, bunyaviridae, ssRNA negative- strand viruses, antiparallel coiled coil, viral protein; 1.15A {Sin nombre virus}

Probab=85.95  E-value=1.8  Score=33.86  Aligned_cols=50  Identities=24%  Similarity=0.354  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022306          105 ELVALREQVEDLQRKMFEKDEL---------LKSLESSKSQVNAVHLKLDELKRLAAEK  154 (299)
Q Consensus       105 El~~LreQVeeLqkKL~EKDel---------LkSae~~~~em~a~~akvDELr~~laeK  154 (299)
                      |+-...-|+---++||-+=...         ..++......+++++.||.+|++++|+.
T Consensus        13 e~~~~E~QL~~A~QKLkdA~~~~e~DPDevNK~~~~~R~~~V~~lq~Ki~elkrqlAd~   71 (78)
T 2ic6_A           13 NITLHEQRLVTTRQKLKDAERAVELDPDDVNKSTLQSRRAAVSALETKLGELKRELADL   71 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444445555555555433222         3345555688888888888888888875

>4fi5_A Nucleoprotein; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.20A {Hantaan virus}

Probab=85.74  E-value=2  Score=35.64  Aligned_cols=54  Identities=22%  Similarity=0.265  Sum_probs=39.9

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhhHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Q 022306          102 EIEELVALREQVEDLQRKMFEKDEL---------LKSLESSKSQVNAVHLKLDELKRLAAEKD  155 (299)
Q Consensus       102 ~~eEl~~LreQVeeLqkKL~EKDel---------LkSae~~~~em~a~~akvDELr~~laeKe  155 (299)
                      --+|+....-|+---++||-+=...         ..++......+++++.||+||++++|+.=
T Consensus        27 Lq~Ei~~~E~QL~~ArQKLkdA~~~~e~DPDevNK~tl~~R~~~Vs~lq~KiaeLKrqLAd~v   89 (113)
T 4fi5_A           27 LQREINAHEGQLVIARQKVRDAEKQYEKDPDELNKRTLTDREGVAVSIQAKIDELKRQLADRI   89 (113)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456777777777777777654433         34666677899999999999999998864

>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=83.43  E-value=6.6  Score=30.10  Aligned_cols=53  Identities=13%  Similarity=0.228  Sum_probs=26.3

Q ss_pred             HhhHHHHhhhhHHHHHHHHHHHHHHhhhHHHHHHHHHhhhhhhHHHHHHHHhh
Q 022306          164 QLSDAKIKLADKQAALEKSQWEAMTVSRKAEKLQEEVESMQGEMSSFMQIFEG  216 (299)
Q Consensus       164 QLsdaki~LadKqAaLEKlewE~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~  216 (299)
                      ++.+.+..+....+.|.++..+.-.-.+--..|=+==-.++.||++.+.+|++
T Consensus        29 ~l~~~q~~i~~lE~el~~~r~e~~~ql~EYq~LlnvK~~Le~EIatYRkLLEG   81 (86)
T 1x8y_A           29 ERDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEG   81 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHcC
Confidence            33344444444444444444443332222222222223567899999998885

>2b9c_A Striated-muscle alpha tropomyosin; alpha-helix, coiled coil, alanine, axial stagger, radius, SIDE-chain packing, crystal packing; 2.30A {Rattus norvegicus} SCOP: h.1.5.1

Probab=82.82  E-value=20  Score=30.09  Aligned_cols=110  Identities=18%  Similarity=0.238  Sum_probs=85.9

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhhHHHHHHHHHHH
Q 022306          106 LVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLADKQAALEKSQWE  185 (299)
Q Consensus       106 l~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~LadKqAaLEKlewE  185 (299)
                      |.....++++..+..-|-+..++.+++..   ..-..+|+.|-.+|.+=....+.+---..++--+|+-...-|++.+--
T Consensus        19 l~~a~~kLeeaek~adE~eR~~k~lE~r~---~~deEr~~~lE~qLkeak~~aeeadrKyeE~~RKl~~~E~dLeraeeR   95 (147)
T 2b9c_A           19 LATALQKLEEAEKAADESERGMKVIESRA---QKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEER   95 (147)
T ss_dssp             TTHHHHHHHHHHHHHHHHTHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhh---cccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            44556777888888877777777766553   344556677777777666777777777888888999999999999999


Q ss_pred             HHHhhhHHHHHHHHHhhhhhhHHHHHHHHhhhh
Q 022306          186 AMTVSRKAEKLQEEVESMQGEMSSFMQIFEGLI  218 (299)
Q Consensus       186 ~~~sn~Kve~Lq~dl~~m~~eIsslm~~fe~lt  218 (299)
                      +-....|+-.|+++|..+...+-+|....++-+
T Consensus        96 ae~aE~k~~eLEeeL~~~~~nlKsLE~~eekas  128 (147)
T 2b9c_A           96 AELSEGKCAELEEELKTVTNNLKSLEDKVEELL  128 (147)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHH
Confidence            999999999999999999999998876555433

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=82.22  E-value=16  Score=28.43  Aligned_cols=53  Identities=9%  Similarity=0.164  Sum_probs=26.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhhhh
Q 022306          122 EKDELLKSLESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKLAD  174 (299)
Q Consensus       122 EKDelLkSae~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~Lad  174 (299)
                      |||.++.-++....++..+......+-.++..=-.=|+.++.+|-.+...|.+
T Consensus        17 e~e~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~eld~~~e~l~~   69 (101)
T 3u59_A           17 DKENAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEKYSESVKE   69 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56666666666665555555544444444443333344444444444444433

>2ic9_A Nucleocapsid protein; hantavirus, bunyaviridae, ssRNA negative- strand viruses, antiparallel coiled coil, viral protein; 2.00A {Sin nombre virus}

Probab=82.19  E-value=3.5  Score=33.32  Aligned_cols=52  Identities=23%  Similarity=0.334  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Q 022306          104 EELVALREQVEDLQRKMFEKDEL---------LKSLESSKSQVNAVHLKLDELKRLAAEKD  155 (299)
Q Consensus       104 eEl~~LreQVeeLqkKL~EKDel---------LkSae~~~~em~a~~akvDELr~~laeKe  155 (299)
                      +|+-...-|+---++||-+=...         ..++.+....+++++.||.+|++++|+.=
T Consensus        12 ~e~~~~E~QL~~A~QKLkdA~~~~e~DPDevNk~~~~~R~~~V~~lq~Ki~elkr~lAd~v   72 (96)
T 2ic9_A           12 DNITLHEQRLVTTRQKLKDAERAVELDPDDVNKSTLQSRRAAVSALETKLGELKRELADLI   72 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555433222         33455556888888888888888888753

>2p22_C Protein SRN2; endosome, trafficking complex, VPS23, VPS28, VPS37, MVB12; 2.70A {Saccharomyces cerevisiae} PDB: 2caz_C 2f66_C

Probab=81.68  E-value=26  Score=30.61  Aligned_cols=88  Identities=10%  Similarity=0.090  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhHHhhHHHHhh-------hhHHHHHHHHHHHHHHhhhHHHHHHHHHhhh
Q 022306          131 ESSKSQVNAVHLKLDELKRLAAEKDSLIKSTQLQLSDAKIKL-------ADKQAALEKSQWEAMTVSRKAEKLQEEVESM  203 (299)
Q Consensus       131 e~~~~em~a~~akvDELr~~laeKe~likStq~QLsdaki~L-------adKqAaLEKlewE~~~sn~Kve~Lq~dl~~m  203 (299)
                      .+..+++..+...++++|.++-++=.-++++..+.+.....+       =.-.+.+++|+-.+..++..++.|......-
T Consensus        75 ~s~ae~ll~l~~~Le~~r~~l~~~l~~~~~L~~~~~~k~q~~~~~ls~~~sp~~L~~~L~~a~~e~eeeS~~l~~~F~~~  154 (192)
T 2p22_C           75 RDQFKQLEENFEDLHEQKDKVQALLENARILESKYVASWQDYHSEFSKKYGDIALKKKLEQNTKKLDEESSQLETTTRSI  154 (192)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHSCSCC
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            444445556666666666666666666666666665444333       1235788999999999999999999999764


Q ss_pred             --hhhHHHHHHHHhhhh
Q 022306          204 --QGEMSSFMQIFEGLI  218 (299)
Q Consensus       204 --~~eIsslm~~fe~lt  218 (299)
                        .-+|..|...|..+.
T Consensus       155 ~~e~dv~~Fl~~y~~~R  171 (192)
T 2p22_C          155 DSADDLDQFIKNYLDIR  171 (192)
T ss_dssp             CCHHHHHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHHH
Confidence              457778888887654

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=80.87  E-value=14  Score=30.41  Aligned_cols=53  Identities=26%  Similarity=0.310  Sum_probs=41.0

Q ss_pred             hhhcHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022306           99 SEKEIEELVALREQVEDLQRKMFEKDELLKSLESSKSQVNAVHLKLDELKRLA  151 (299)
Q Consensus        99 ~~k~~eEl~~LreQVeeLqkKL~EKDelLkSae~~~~em~a~~akvDELr~~l  151 (299)
                      +..++.|+..|..++....+.|.+|...+.-++....+..+...+|.=|+.|+
T Consensus        19 ~~~~~~ei~~L~~~L~~AEeaL~~Kq~~idelk~ei~q~~~~lE~I~vLkaQv   71 (110)
T 2v4h_A           19 SHMASMQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIVMETVPVLKAQA   71 (110)
T ss_dssp             CCSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHH
T ss_pred             hHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34466689999999999999999998888888887777666666766666664

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

No hit with probability above 80.00