Citrus Sinensis ID: 022126

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300--
Protein Sequence
MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSAIQPSNSFYPRNDPDLFSANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSNSGPFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRPQLSRNRTQIFTL
Secondary Structure (PSIPRED)
cccccccccccccEEEccccccccccHHHHHcccccccccccccccccccccccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHcccEEEEccccEEcHHHHHHHcccccccccccccccccccEEccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccEEEccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccEEcc
Coil and Loop (DISEMBL)
MRCNACWRELEGRAISTTCGHLLCTEDANkilsndaacpicdqvlskslmkpvdinpndewVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKrsaiqpsnsfyprndpdlfsanmmdnrdpirkdwsvyspgtpgprediwparqnssnsgpfdiatgspakqpvipvdggnrradarpafgggaanpsmtLRNLilspikrpqlsrnrtqiftl
Flexible Loop (DISEMBL)
mrcnacwrELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKfseksrqkrkldemYDQLRSEYESMkrsaiqpsnsfypRNDPDLFSANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSNSGPFDIATGSPAKQPVIPVDGGNRRADArpafgggaanpsmTLRNLIlspikrpqlsrnrtqiftl
Low Complexity Region (SEG)
MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSAIQPSNSFYPRNDPDLFSANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSNSGPFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRPQLSRNRTQIFTL
Disordered region (IsUnstruct)
**CNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHT**********************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNR***QCRQKCEAMQEKF****EQ**********************************************************************************************************************************************************************************F**
Disordered Region (DISEMBL)
MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIES*********************LDEMYDQLRSEYESMKRSAIQPSNSFYPRNDPDLFSANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSNSGPFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRPQLSRNRTQIFTL
Disordered Region (DISPRO)
MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSAIQPSNSFYPRNDPDLFSAN**D*R*****DWSVYSPGTPGPREDIWPARQNSSNSGP**IAT*SPAKQPVIPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRP*L**********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAIQPSNSFYPRNDPDLFSANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSNSGPFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRPQLSRNRTQIFTL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	302	2.2.26 [Sep-21-2011]
Q9NPC3	277	E3 ubiquitin-protein liga	yes	no	0.556	0.606	0.268	1e-14

>sp|Q9NPC3|CIP1_HUMAN E3 ubiquitin-protein ligase CCNB1IP1 OS=Homo sapiens GN=CCNB1IP1 PE=1 SV=1

 Score = 80.5 bits (197), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 48/179 (26%), Positives = 92/179 (51%), Gaps = 11/179 (6%)

Query: 1   MRCN--ACWRELEGRAISTTCGHLLCTEDANKILSND-AACPICDQVLSKSL-MKPVDIN 56
           + CN   C  +L G A  T C H+ C +  +   S   A CP C+  LS  L +   +++
Sbjct: 8   LLCNYRKCRIKLSGYAWVTACSHIFCDQHGSGEFSRSPAICPACNSTLSGKLDIVRTELS 67

Query: 57  PNDEWVNMAMAGVSPQILMKSAYRSVMFY---LGQKELEMQYKMNRIVAQCRQKCEAMQE 113
           P++E+  M +AG+ P+I++  + R++ F+   + Q+ L  +Y  ++     +Q    M++
Sbjct: 68  PSEEYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSKAEGHLKQ----MEK 123

Query: 114 KFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLR 172
            +T++++        M      M++ +E   K   ++ EK  E++RQ +KL  +YD LR
Sbjct: 124 IYTQQIQSKDVELTSMKGEVTSMKKVLEEYKKKFSDISEKLMERNRQYQKLQGLYDSLR 182

E3 ubiquitin-protein ligase. Modulates cyclin B levels and participates in the regulation of cell cycle progression through the G2 phase. Overexpression causes delayed entry into mitosis.
Homo sapiens (taxid: 9606)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

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	302
224118990	301	predicted protein [Populus trichocarpa]	0.986	0.990	0.839	1e-150
225461800	301	PREDICTED: uncharacterized protein LOC10	0.986	0.990	0.848	1e-149
356556629	304	PREDICTED: uncharacterized protein LOC10	0.996	0.990	0.822	1e-146
356530649	304	PREDICTED: uncharacterized protein LOC10	0.996	0.990	0.812	1e-145
449438901	304	PREDICTED: uncharacterized protein LOC10	0.996	0.990	0.809	1e-144
145336703	304	RING/U-box domain-containing protein [Ar	0.986	0.980	0.795	1e-142
297847746	303	predicted protein [Arabidopsis lyrata su	0.983	0.980	0.791	1e-138
386302981	304	HEI10 [Oryza sativa Japonica Group]	0.993	0.986	0.732	1e-127
222622480	336	hypothetical protein OsJ_05990 [Oryza sa	0.990	0.889	0.731	1e-127
115445183	303	Os02g0232100 [Oryza sativa Japonica Grou	0.990	0.986	0.731	1e-127

>gi|224118990|ref|XP_002331298.1| predicted protein [Populus trichocarpa] gi|222873881|gb|EEF11012.1| predicted protein [Populus trichocarpa]

 Score =  538 bits (1386), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 256/305 (83%), Positives = 280/305 (91%), Gaps = 7/305 (2%)

Query: 1   MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
           MRCN+CWRELEGRA+STTCG    TEDANKIL+NDAACPICDQVLSKSLMKPV+INPNDE
Sbjct: 1   MRCNSCWRELEGRAVSTTCG----TEDANKILNNDAACPICDQVLSKSLMKPVEINPNDE 56

Query: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
           W+NMAMAG+SPQILMKSAYRSVMF+ GQ+ELEMQYKMNRIVAQCRQKCE+MQEKFTEKLE
Sbjct: 57  WINMAMAGISPQILMKSAYRSVMFFTGQRELEMQYKMNRIVAQCRQKCESMQEKFTEKLE 116

Query: 121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           Q+H AYQKMAKRCQMMEQEIESLSKDKQELQEKFSEK+RQKRKLDEMYDQLRSEYES KR
Sbjct: 117 QLHAAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKARQKRKLDEMYDQLRSEYESNKR 176

Query: 181 SAIQPSNSFYPRNDPDLFS---ANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSNS 237
           SAIQP+N+F+ RN+PDLFS   A MMDNRDPIRKDW+V++P TPGPREDIWPARQNSSNS
Sbjct: 177 SAIQPANNFFSRNEPDLFSNPAATMMDNRDPIRKDWTVFTPSTPGPREDIWPARQNSSNS 236

Query: 238 GPFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRPQLSRNRT 297
           GPF+I  GSPA Q  +PVD GNRR  A P+FG G+ NPSMTLRNLILSPIKRPQLSR+R 
Sbjct: 237 GPFEIRGGSPANQAAMPVDVGNRRIGAVPSFGAGSGNPSMTLRNLILSPIKRPQLSRSRP 296

Query: 298 QIFTL 302
           Q+FTL
Sbjct: 297 QMFTL 301

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461800|ref|XP_002285631.1| PREDICTED: uncharacterized protein LOC100243485 [Vitis vinifera] gi|302142815|emb|CBI20110.3| unnamed protein product [Vitis vinifera]

 Score =  535 bits (1377), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 258/304 (84%), Positives = 278/304 (91%), Gaps = 6/304 (1%)

Query: 1   MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
           MRCNACWRELEGRAISTTCGHLLC+EDA+KILS+DAACPICDQVLSKSLMKPVD+NPNDE
Sbjct: 1   MRCNACWRELEGRAISTTCGHLLCSEDASKILSSDAACPICDQVLSKSLMKPVDVNPNDE 60

Query: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
           W+NMAMAGVSPQILMKSAYRSVMFY+GQKELEMQYKMNRIVAQCRQKCE MQEKFTEKLE
Sbjct: 61  WINMAMAGVSPQILMKSAYRSVMFYIGQKELEMQYKMNRIVAQCRQKCEMMQEKFTEKLE 120

Query: 121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           QVHTAYQKMAKRCQMMEQEIE++SKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR
Sbjct: 121 QVHTAYQKMAKRCQMMEQEIETMSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180

Query: 181 SAIQPSNSFYPRNDPDLFS--ANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSNS- 237
           SAIQP+ +FY R +PDLFS   N+MDNRD IRKDWSV++P TPGP+EDIW ARQNSSNS 
Sbjct: 181 SAIQPTTNFYSRPEPDLFSNQPNIMDNRDTIRKDWSVFTPETPGPKEDIWTARQNSSNSG 240

Query: 238 GPFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRPQLSRNRT 297
           GPF+++ GSP KQ  I VD GNRRA    AFG GA NPSMT+RNLILSPIKRPQLSR R 
Sbjct: 241 GPFEVSGGSPMKQARISVDAGNRRAG---AFGTGAGNPSMTIRNLILSPIKRPQLSRGRP 297

Query: 298 QIFT 301
            +FT
Sbjct: 298 NMFT 301

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556629|ref|XP_003546626.1| PREDICTED: uncharacterized protein LOC100783938 [Glycine max]

 Score =  524 bits (1350), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 250/304 (82%), Positives = 276/304 (90%), Gaps = 3/304 (0%)

Query: 1   MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
           MRCNACWRE+EGRAISTTCGHLLCT+DANKILSND ACPICDQVLSKSLMKPVD+NPNDE
Sbjct: 1   MRCNACWREVEGRAISTTCGHLLCTDDANKILSNDGACPICDQVLSKSLMKPVDVNPNDE 60

Query: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
           WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQ+KMN+IVAQCRQKCE MQEKFTEK+E
Sbjct: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQFKMNKIVAQCRQKCEMMQEKFTEKIE 120

Query: 121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           QVHTAYQKMAK+CQMM+QEIESL+KD QELQEKF+EKSRQKRKLDEMYDQLR+EY+S+KR
Sbjct: 121 QVHTAYQKMAKKCQMMQQEIESLTKDNQELQEKFAEKSRQKRKLDEMYDQLRNEYDSVKR 180

Query: 181 SAIQPSNSFYPRNDPDLFS--ANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSNSG 238
           SAIQP+++FY RN+ DLFS   N+MD R+  RK   V++P TPGPRED+WPARQNS+NSG
Sbjct: 181 SAIQPADNFYSRNEHDLFSNPPNIMDGREMGRKGGLVFTPATPGPREDVWPARQNSNNSG 240

Query: 239 PFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAA-NPSMTLRNLILSPIKRPQLSRNRT 297
            FD++ GSPAKQ VI  D GNRRA A P FG GA  NPSMTLRNLILSPIKRPQLSRNR 
Sbjct: 241 HFDLSVGSPAKQTVIAGDAGNRRAGAHPVFGPGATNNPSMTLRNLILSPIKRPQLSRNRP 300

Query: 298 QIFT 301
           Q+FT
Sbjct: 301 QLFT 304

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530649|ref|XP_003533893.1| PREDICTED: uncharacterized protein LOC100810502 [Glycine max]

 Score =  521 bits (1341), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 247/304 (81%), Positives = 276/304 (90%), Gaps = 3/304 (0%)

Query: 1   MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
           MRCNACWRE+EGRAISTTCGHLLCT+DANKILSND ACPICDQVLSKSLMKPVD+NPNDE
Sbjct: 1   MRCNACWREVEGRAISTTCGHLLCTDDANKILSNDGACPICDQVLSKSLMKPVDVNPNDE 60

Query: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
           WVNMAMAGVSPQILMKSAYRSVMFY+GQKELE+Q+KMN+IVAQCRQKCE MQEKFTEKLE
Sbjct: 61  WVNMAMAGVSPQILMKSAYRSVMFYMGQKELEIQFKMNKIVAQCRQKCETMQEKFTEKLE 120

Query: 121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           QVHTAYQKMAK+CQMM+QEIES++KD QELQEKF+EKSRQKRKLDEMYDQLR+EY+S+KR
Sbjct: 121 QVHTAYQKMAKKCQMMQQEIESITKDNQELQEKFAEKSRQKRKLDEMYDQLRNEYDSVKR 180

Query: 181 SAIQPSNSFYPRNDPDLFS--ANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSNSG 238
            AIQP+N+FY RN+ DLFS   N+MD+R+  RK   V++P TPGPRED+WPARQNS+NSG
Sbjct: 181 FAIQPANNFYARNEHDLFSNPPNIMDDREMGRKGGLVFTPATPGPREDVWPARQNSNNSG 240

Query: 239 PFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAA-NPSMTLRNLILSPIKRPQLSRNRT 297
            FD++ GSPAKQ VI  D G+RRA A P FG GA  NPSMTLRNLILSPIKRPQLSRNR 
Sbjct: 241 HFDLSVGSPAKQTVIAGDAGSRRAGAHPVFGPGATNNPSMTLRNLILSPIKRPQLSRNRP 300

Query: 298 QIFT 301
           Q+FT
Sbjct: 301 QLFT 304

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438901|ref|XP_004137226.1| PREDICTED: uncharacterized protein LOC101209267 [Cucumis sativus] gi|449483181|ref|XP_004156515.1| PREDICTED: uncharacterized protein LOC101230782 [Cucumis sativus]

 Score =  518 bits (1334), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 247/305 (80%), Positives = 273/305 (89%), Gaps = 4/305 (1%)

Query: 1   MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
           M+CNACWRELEGRA++TTCGHLLCTEDA+KILSND ACPICDQVLSKSLMKPVDINPNDE
Sbjct: 1   MKCNACWRELEGRAVTTTCGHLLCTEDASKILSNDGACPICDQVLSKSLMKPVDINPNDE 60

Query: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
           W NMAMAG+SPQILMKSAYRSVMFY GQKELEMQYKMNR++AQCRQKCE MQEKFTEKLE
Sbjct: 61  WANMAMAGISPQILMKSAYRSVMFYNGQKELEMQYKMNRLMAQCRQKCEVMQEKFTEKLE 120

Query: 121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           QVH+AYQKMAKRCQMME+E+E+LSKDKQELQEKF+EKSRQKRKLDEMYDQLR+E+ES+KR
Sbjct: 121 QVHSAYQKMAKRCQMMEREMENLSKDKQELQEKFAEKSRQKRKLDEMYDQLRNEHESLKR 180

Query: 181 SAIQPSNSFYPRNDPDLFS--ANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSNSG 238
           SAIQP  +FY RN+ DLFS   N+MDNR+  RKDW V +P TPGPRE+IWP RQNS NSG
Sbjct: 181 SAIQPVTNFYTRNESDLFSNPVNLMDNREATRKDWMVSAPETPGPREEIWPTRQNSGNSG 240

Query: 239 PFDIATGSPAKQPV-IPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRPQLSRNRT 297
            FDI+ GSPAKQ   + ++ GNRRA A  AFG GA NPSMTLRNLILSPIKRPQLSR R 
Sbjct: 241 HFDISVGSPAKQAAPMAMEAGNRRAGAHTAFGSGAGNPSMTLRNLILSPIKRPQLSR-RP 299

Query: 298 QIFTL 302
           Q+FTL
Sbjct: 300 QMFTL 304

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145336703|ref|NP_175754.2| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|332194827|gb|AEE32948.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score =  508 bits (1309), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 245/308 (79%), Positives = 275/308 (89%), Gaps = 10/308 (3%)

Query: 1   MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
           MRCNACWR+LEGRAISTTCGHLLCTEDA+KILSND ACPICDQVLSKSLMKPVDINPN+E
Sbjct: 1   MRCNACWRDLEGRAISTTCGHLLCTEDASKILSNDGACPICDQVLSKSLMKPVDINPNEE 60

Query: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
           W+NMAMAG+SPQILMKSAYRSVMFY+ Q++LEMQYKMNR+VAQCRQKCE MQ KF+EK+E
Sbjct: 61  WINMAMAGISPQILMKSAYRSVMFYIAQRDLEMQYKMNRVVAQCRQKCEGMQAKFSEKME 120

Query: 121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           QVHTAYQKM KRCQMMEQE+E+L+KDKQELQEKFSEKSRQKRKLDEMYDQLRSEYES+KR
Sbjct: 121 QVHTAYQKMGKRCQMMEQEVENLTKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESVKR 180

Query: 181 SAIQPSNSFYPRN-DPDLFS---ANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSN 236
           +AIQP+N+FYPR+ +PD FS    NMM+NR+ IRKD S +SP TPGP+++IWPARQNSSN
Sbjct: 181 TAIQPANNFYPRHQEPDFFSNPAVNMMENRETIRKDRSFFSPATPGPKDEIWPARQNSSN 240

Query: 237 SGPFDIATGSPAKQPVIPVDGGNRRAD-ARPAFGGGA-ANPSMTLRNLILSPIKRPQLSR 294
           SGPFDI+T SPA    IP D GNRRA    P +GGG  ANP  TLRNLILSPIKR QLSR
Sbjct: 241 SGPFDISTDSPA----IPSDLGNRRAGRGHPVYGGGGTANPQSTLRNLILSPIKRSQLSR 296

Query: 295 NRTQIFTL 302
           +R Q+FTL
Sbjct: 297 SRPQLFTL 304

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297847746|ref|XP_002891754.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297337596|gb|EFH68013.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  497 bits (1280), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 243/307 (79%), Positives = 273/307 (88%), Gaps = 10/307 (3%)

Query: 1   MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
           MRCNACWR+LEGRAISTTCGHLLCTEDA+KILSND ACPICDQVLSKSLMKPVDINPN+E
Sbjct: 1   MRCNACWRDLEGRAISTTCGHLLCTEDASKILSNDGACPICDQVLSKSLMKPVDINPNEE 60

Query: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
           W+NMAMAG+SPQILMKSAYRSVMFY+ Q++LEMQYKMNR+VAQCRQKCE MQ KF+EK+E
Sbjct: 61  WINMAMAGISPQILMKSAYRSVMFYIAQRDLEMQYKMNRVVAQCRQKCEGMQAKFSEKME 120

Query: 121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           QVHTAYQKM KRCQMMEQE+E+L+KDKQELQEKFSEKSRQKRKLDEMYDQLRSEYES+KR
Sbjct: 121 QVHTAYQKMGKRCQMMEQEVENLTKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESVKR 180

Query: 181 SAIQPSNSFYPRN-DPDLFS---ANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSN 236
           +AIQP+N+FYPR+ +PD FS    NMM+NR+PIRKD S +SP TPGP+++IWPARQNSSN
Sbjct: 181 TAIQPANNFYPRHQEPDFFSNPAVNMMENREPIRKDRSFFSPATPGPKDEIWPARQNSSN 240

Query: 237 SGPFDIATGSPAKQPVIPVDGGNRRA--DARPAFGGGAANPSMTLRNLILSPIKRPQLSR 294
           SGPFDI+T SPA    IP D GNRRA        GGG +NP  TLRNLILSPIKR QLSR
Sbjct: 241 SGPFDISTDSPA----IPSDLGNRRAGGGHPVYGGGGTSNPQSTLRNLILSPIKRSQLSR 296

Query: 295 NRTQIFT 301
           +R Q+FT
Sbjct: 297 SRPQLFT 303

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|386302981|gb|AFJ04809.1| HEI10 [Oryza sativa Japonica Group]

 Score =  461 bits (1187), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 224/306 (73%), Positives = 257/306 (83%), Gaps = 6/306 (1%)

Query: 1   MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
           M+CNACWRELEG+A+STTCGHLLCTEDA KILSNDAACPICDQVLSKS M+PVD NPND+
Sbjct: 1   MKCNACWRELEGQAVSTTCGHLLCTEDAKKILSNDAACPICDQVLSKSHMRPVDTNPNDD 60

Query: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
           W NM+MAGVSPQILMKSAYRSVMFY+GQKELEMQYKMNRIV QCRQKCE MQ KFTEKLE
Sbjct: 61  WTNMSMAGVSPQILMKSAYRSVMFYIGQKELEMQYKMNRIVGQCRQKCELMQAKFTEKLE 120

Query: 121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           +VHTAYQKMAK+CQ+MEQE+E+LS+DKQELQEKF+EKSRQKRKLDEMYDQLRSEYES KR
Sbjct: 121 EVHTAYQKMAKKCQLMEQEVENLSRDKQELQEKFAEKSRQKRKLDEMYDQLRSEYESAKR 180

Query: 181 SAIQPSNSFYPRNDPDLFSA--NMMDNRDPIRKDWSVYSPGTPGPREDIW--PARQNSSN 236
           SAIQP+N+++PR  PDLFS   N+MD+ DP+R+  +   P TPG R++ W  P RQ  S 
Sbjct: 181 SAIQPANNYFPRAQPDLFSGVPNIMDSSDPLRQGLAGL-PETPGRRDEGWAPPPRQRRST 239

Query: 237 SGPFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRPQLSRNR 296
           SGPF+++ GSPA     PVD   R+  ARP FG    N S  LRN+I+SP+KRPQLSRNR
Sbjct: 240 SGPFELSAGSPAHNAAPPVDIRPRQP-ARPVFGTAMNNTSAALRNMIISPVKRPQLSRNR 298

Query: 297 TQIFTL 302
             +FTL
Sbjct: 299 PHMFTL 304

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222622480|gb|EEE56612.1| hypothetical protein OsJ_05990 [Oryza sativa Japonica Group]

 Score =  461 bits (1186), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 223/305 (73%), Positives = 256/305 (83%), Gaps = 6/305 (1%)

Query: 1   MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
           M+CNACWRELEG+A+STTCGHLLCTEDA KILSNDAACPICDQVLSKS M+PVD NPND+
Sbjct: 34  MKCNACWRELEGQAVSTTCGHLLCTEDAKKILSNDAACPICDQVLSKSHMRPVDTNPNDD 93

Query: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
           W NM+MAGVSPQILMKSAYRSVMFY+GQKELEMQYKMNRIV QCRQKCE MQ KFTEKLE
Sbjct: 94  WTNMSMAGVSPQILMKSAYRSVMFYIGQKELEMQYKMNRIVGQCRQKCELMQAKFTEKLE 153

Query: 121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           +VHTAYQKMAK+CQ+MEQE+E+LS+DKQELQEKF+EKSRQKRKLDEMYDQLRSEYES KR
Sbjct: 154 EVHTAYQKMAKKCQLMEQEVENLSRDKQELQEKFAEKSRQKRKLDEMYDQLRSEYESAKR 213

Query: 181 SAIQPSNSFYPRNDPDLFSA--NMMDNRDPIRKDWSVYSPGTPGPREDIW--PARQNSSN 236
           SAIQP+N+++PR  PDLFS   N+MD+ DP+R+  +   P TPG R++ W  P RQ  S 
Sbjct: 214 SAIQPANNYFPRAQPDLFSGVPNIMDSSDPLRQGLAGL-PETPGRRDEGWAPPPRQRRST 272

Query: 237 SGPFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRPQLSRNR 296
           SGPF+++ GSPA     PVD   R+  ARP FG    N S  LRN+I+SP+KRPQLSRNR
Sbjct: 273 SGPFELSAGSPAHNAAPPVDIRPRQP-ARPVFGTAMNNTSAALRNMIISPVKRPQLSRNR 331

Query: 297 TQIFT 301
             +FT
Sbjct: 332 PHMFT 336

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115445183|ref|NP_001046371.1| Os02g0232100 [Oryza sativa Japonica Group] gi|50251774|dbj|BAD27706.1| putative bZIP protein [Oryza sativa Japonica Group] gi|113535902|dbj|BAF08285.1| Os02g0232100 [Oryza sativa Japonica Group]

 Score =  460 bits (1183), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 223/305 (73%), Positives = 256/305 (83%), Gaps = 6/305 (1%)

Query: 1   MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
           M+CNACWRELEG+A+STTCGHLLCTEDA KILSNDAACPICDQVLSKS M+PVD NPND+
Sbjct: 1   MKCNACWRELEGQAVSTTCGHLLCTEDAKKILSNDAACPICDQVLSKSHMRPVDTNPNDD 60

Query: 61  WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
           W NM+MAGVSPQILMKSAYRSVMFY+GQKELEMQYKMNRIV QCRQKCE MQ KFTEKLE
Sbjct: 61  WTNMSMAGVSPQILMKSAYRSVMFYIGQKELEMQYKMNRIVGQCRQKCELMQAKFTEKLE 120

Query: 121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           +VHTAYQKMAK+CQ+MEQE+E+LS+DKQELQEKF+EKSRQKRKLDEMYDQLRSEYES KR
Sbjct: 121 EVHTAYQKMAKKCQLMEQEVENLSRDKQELQEKFAEKSRQKRKLDEMYDQLRSEYESAKR 180

Query: 181 SAIQPSNSFYPRNDPDLFSA--NMMDNRDPIRKDWSVYSPGTPGPREDIW--PARQNSSN 236
           SAIQP+N+++PR  PDLFS   N+MD+ DP+R+  +   P TPG R++ W  P RQ  S 
Sbjct: 181 SAIQPANNYFPRAQPDLFSGVPNIMDSSDPLRQGLAGL-PETPGRRDEGWAPPPRQRRST 239

Query: 237 SGPFDIATGSPAKQPVIPVDGGNRRADARPAFGGGAANPSMTLRNLILSPIKRPQLSRNR 296
           SGPF+++ GSPA     PVD   R+  ARP FG    N S  LRN+I+SP+KRPQLSRNR
Sbjct: 240 SGPFELSAGSPAHNAAPPVDIRPRQP-ARPVFGTAMNNTSAALRNMIISPVKRPQLSRNR 298

Query: 297 TQIFT 301
             +FT
Sbjct: 299 PHMFT 303

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	302
TAIR|locus:2024917	304	HEI10 "AT1G53490" [Arabidopsis	0.986	0.980	0.795	1.9e-131
DICTYBASE|DDB_G0269498	350	DDB_G0269498 "RING zinc finger	0.602	0.52	0.286	3.6e-19
RGD|1561930	276	Ccnb1ip1 "cyclin B1 interactin	0.649	0.710	0.258	5.3e-17
UNIPROTKB|Q2YDD5	277	CCNB1IP1 "Uncharacterized prot	0.596	0.649	0.264	8.6e-17
UNIPROTKB|Q9NPC3	277	CCNB1IP1 "E3 ubiquitin-protein	0.549	0.599	0.271	1.4e-16
UNIPROTKB|F1S8F8	277	CCNB1IP1 "Uncharacterized prot	0.549	0.599	0.271	1.4e-16
UNIPROTKB|E2RHZ9	336	CCNB1IP1 "Uncharacterized prot	0.596	0.535	0.269	3.6e-16
UNIPROTKB|G3V5S3	154	CCNB1IP1 "E3 ubiquitin-protein	0.447	0.876	0.246	1.3e-09
UNIPROTKB|E1BV34	582	Gga.3145 "Uncharacterized prot	0.403	0.209	0.259	0.00069

TAIR|locus:2024917 HEI10 "AT1G53490" [Arabidopsis thaliana (taxid:3702)]

 Score = 1289 (458.8 bits), Expect = 1.9e-131, P = 1.9e-131
 Identities = 245/308 (79%), Positives = 275/308 (89%)

Query:     1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE 60
             MRCNACWR+LEGRAISTTCGHLLCTEDA+KILSND ACPICDQVLSKSLMKPVDINPN+E
Sbjct:     1 MRCNACWRDLEGRAISTTCGHLLCTEDASKILSNDGACPICDQVLSKSLMKPVDINPNEE 60

Query:    61 WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLE 120
             W+NMAMAG+SPQILMKSAYRSVMFY+ Q++LEMQYKMNR+VAQCRQKCE MQ KF+EK+E
Sbjct:    61 WINMAMAGISPQILMKSAYRSVMFYIAQRDLEMQYKMNRVVAQCRQKCEGMQAKFSEKME 120

Query:   121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
             QVHTAYQKM KRCQMMEQE+E+L+KDKQELQEKFSEKSRQKRKLDEMYDQLRSEYES+KR
Sbjct:   121 QVHTAYQKMGKRCQMMEQEVENLTKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESVKR 180

Query:   181 SAIQPSNSFYPRN-DPDLFS---ANMMDNRDPIRKDWSVYSPGTPGPREDIWPARQNSSN 236
             +AIQP+N+FYPR+ +PD FS    NMM+NR+ IRKD S +SP TPGP+++IWPARQNSSN
Sbjct:   181 TAIQPANNFYPRHQEPDFFSNPAVNMMENRETIRKDRSFFSPATPGPKDEIWPARQNSSN 240

Query:   237 SGPFDIATGSPAKQPVIPVDGGNRRAD-ARPAFGGGA-ANPSMTLRNLILSPIKRPQLSR 294
             SGPFDI+T SPA    IP D GNRRA    P +GGG  ANP  TLRNLILSPIKR QLSR
Sbjct:   241 SGPFDISTDSPA----IPSDLGNRRAGRGHPVYGGGGTANPQSTLRNLILSPIKRSQLSR 296

Query:   295 NRTQIFTL 302
             +R Q+FTL
Sbjct:   297 SRPQLFTL 304

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0007126 "meiosis" evidence=IMP

GO:0035825 "reciprocal DNA recombination" evidence=IMP

GO:0051026 "chiasma assembly" evidence=IMP

DICTYBASE|DDB_G0269498 DDB_G0269498 "RING zinc finger-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 230 (86.0 bits), Expect = 3.6e-19, P = 3.6e-19
 Identities = 55/192 (28%), Positives = 104/192 (54%)

Query:     1 MRCNACWREL--EGRAISTTCGHLLCTEDA-NKILSNDAACPICDQVL-SKSLMKPVDIN 56
             + CN+CW+E+    R I T+C H+ C   A NK+ ++D  CPICD  L SK  +    I+
Sbjct:     6 IHCNSCWKEIIENDRCIITSCSHIFCDLCASNKLCTDDRLCPICDNSLVSKDSLFGTTID 65

Query:    57 PNDEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFT 116
              + E  N+ + G+SP+ ++  A +++ F+  Q  + +Q      + Q +Q      E+  
Sbjct:    66 SSIE-KNILLFGLSPKKILLMAEKAIEFFNYQTSVYLQ----SYIYQAQQSMNQF-EQLK 119

Query:   117 EKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE 176
             +  E++    + + K+ ++ + + E+  ++  EL EK +EK+RQKRKL+E+Y  L+    
Sbjct:   120 KSNEELIFKIESLEKQLKLQKDDGENDKREIVELTEKLAEKTRQKRKLEELYLSLKENMN 179

Query:   177 SMKRSAIQPSNS 188
             ++  +     N+
Sbjct:   180 NLNNNIKNNDNN 191

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

RGD|1561930 Ccnb1ip1 "cyclin B1 interacting protein 1, E3 ubiquitin protein ligase" [Rattus norvegicus (taxid:10116)]

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 54/209 (25%), Positives = 103/209 (49%)

Query:     3 CN--ACWRELEGRAISTTCGHLLCTEDANKILSNDAA-CPICDQVLSKSL-MKPVDINPN 58
             CN   C  +L G A  T C H+ C +  +   S+  A CP C+  LS  L +   +++P+
Sbjct:    10 CNYRKCRIKLSGYAWVTACSHIFCDQHGSGEFSHSPAICPACNSTLSGKLDIVRTELSPS 69

Query:    59 DEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEK 118
             +E+  M +AG+ P++++  + R++ F+  Q   E  Y+     ++     + M++ +T++
Sbjct:    70 EEYKAMVLAGLRPEVVLDISSRALAFWTYQVHQERLYQEYNF-SKAENHLKQMEKIYTQQ 128

Query:   119 LEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLR------ 172
             ++        M      M++ +E   K   ++ EK  E++RQ +KL  +YD LR      
Sbjct:   129 IQSKDVELTSMKGEVTSMKKVLEEYKKKFSDISEKLMERNRQYQKLQGLYDSLRLRNITI 188

Query:   173 -SEYESMKRSAIQPSNSF-YPRNDPDLFS 199
              S+  S++ + I  S  F +P  +   FS
Sbjct:   189 ASQEGSLEPAMIPQSGVFGFPSGNSSKFS 217

GO:0001825 "blastocyst formation" evidence=IEA;ISO

GO:0006915 "apoptotic process" evidence=IEA;ISO

GO:0007132 "meiotic metaphase I" evidence=IEA;ISO

GO:0007286 "spermatid development" evidence=IEA;ISO

GO:0035265 "organ growth" evidence=IEA;ISO

GO:0051026 "chiasma assembly" evidence=IEA;ISO

UNIPROTKB|Q2YDD5 CCNB1IP1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 51/193 (26%), Positives = 98/193 (50%)

Query:     3 CN--ACWRELEGRAISTTCGHLLCTEDANKILSNDAA-CPICDQVLSKSL-MKPVDINPN 58
             CN   C  +L G A  T C H+ C +  +   S   A CP C+  LS  L +   +++P+
Sbjct:    10 CNYRKCRVKLSGYAWVTACSHIFCDQHGSGEFSRSPAICPACNSTLSGKLDIVRTELSPS 69

Query:    59 DEWVNMAMAGVSPQILMKSAYRSVMFY---LGQKELEMQYKMNRIVAQCRQKCEAMQEKF 115
             +E+  M +AG+ P+I++  + R++ F+   + Q+ L  +Y  ++     +Q    M++ +
Sbjct:    70 EEYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSKAEGHLKQ----MEKIY 125

Query:   116 TEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEY 175
             T++++        M      M++ +E   K   ++ EK  E++RQ +KL  +YD LR   
Sbjct:   126 TQQIQSKDVELTSMKGEVTSMKKVLEEYKKKFSDISEKLMERNRQYQKLQGLYDSLRLRN 185

Query:   176 ESMKR--SAIQPS 186
              ++    S ++PS
Sbjct:   186 ITIANQDSTLEPS 198

GO:0051026 "chiasma assembly" evidence=IEA

GO:0035265 "organ growth" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0007132 "meiotic metaphase I" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0001825 "blastocyst formation" evidence=IEA

UNIPROTKB|Q9NPC3 CCNB1IP1 "E3 ubiquitin-protein ligase CCNB1IP1" [Homo sapiens (taxid:9606)]

 Score = 205 (77.2 bits), Expect = 1.4e-16, P = 1.4e-16
 Identities = 48/177 (27%), Positives = 91/177 (51%)

Query:     3 CN--ACWRELEGRAISTTCGHLLCTEDANKILSNDAA-CPICDQVLSKSL-MKPVDINPN 58
             CN   C  +L G A  T C H+ C +  +   S   A CP C+  LS  L +   +++P+
Sbjct:    10 CNYRKCRIKLSGYAWVTACSHIFCDQHGSGEFSRSPAICPACNSTLSGKLDIVRTELSPS 69

Query:    59 DEWVNMAMAGVSPQILMKSAYRSVMFY---LGQKELEMQYKMNRIVAQCRQKCEAMQEKF 115
             +E+  M +AG+ P+I++  + R++ F+   + Q+ L  +Y  ++     +Q    M++ +
Sbjct:    70 EEYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSKAEGHLKQ----MEKIY 125

Query:   116 TEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLR 172
             T++++        M      M++ +E   K   ++ EK  E++RQ +KL  +YD LR
Sbjct:   126 TQQIQSKDVELTSMKGEVTSMKKVLEEYKKKFSDISEKLMERNRQYQKLQGLYDSLR 182

GO:0016874 "ligase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0001825 "blastocyst formation" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0007132 "meiotic metaphase I" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0035265 "organ growth" evidence=IEA

GO:0051026 "chiasma assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F1S8F8 CCNB1IP1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 205 (77.2 bits), Expect = 1.4e-16, P = 1.4e-16
 Identities = 48/177 (27%), Positives = 91/177 (51%)

Query:     3 CN--ACWRELEGRAISTTCGHLLCTEDANKILSNDAA-CPICDQVLSKSL-MKPVDINPN 58
             CN   C  +L G A  T C H+ C +  +   S   A CP C+  LS  L +   +++P+
Sbjct:    10 CNYRKCRIKLSGYAWVTACSHIFCDQHGSGEFSRSPAICPACNSTLSGKLDIVRTELSPS 69

Query:    59 DEWVNMAMAGVSPQILMKSAYRSVMFY---LGQKELEMQYKMNRIVAQCRQKCEAMQEKF 115
             +E+  M +AG+ P+I++  + R++ F+   + Q+ L  +Y  ++     +Q    M++ +
Sbjct:    70 EEYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSKAEGHLKQ----MEKIY 125

Query:   116 TEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLR 172
             T++++        M      M++ +E   K   ++ EK  E++RQ +KL  +YD LR
Sbjct:   126 TQQIQSKDVELTSMKGEVTSMKKVLEEYKKKFSDISEKLMERNRQYQKLQGLYDSLR 182

GO:0051026 "chiasma assembly" evidence=IEA

GO:0035265 "organ growth" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0007132 "meiotic metaphase I" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0001825 "blastocyst formation" evidence=IEA

UNIPROTKB|E2RHZ9 CCNB1IP1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 213 (80.0 bits), Expect = 3.6e-16, P = 3.6e-16
 Identities = 52/193 (26%), Positives = 99/193 (51%)

Query:     3 CN--ACWRELEGRAISTTCGHLLCTEDANKILSNDAA-CPICDQVLSKSL-MKPVDINPN 58
             CN   C  +L G A  T C H+ C +  +   S   A CP C+  LS  L +   +++P+
Sbjct:    69 CNYRRCRLKLSGYAWVTACSHIFCDQHGSGEFSRSPAICPACNSTLSGKLDIVRTELSPS 128

Query:    59 DEWVNMAMAGVSPQILMKSAYRSVMFY---LGQKELEMQYKMNRIVAQCRQKCEAMQEKF 115
             +E+  M +AG+ P+I++  + R++ F+   + Q+ L  +Y  ++     +Q    M++ +
Sbjct:   129 EEYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSKAEGHLKQ----MEKIY 184

Query:   116 TEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEY 175
             T++++        M      M++ +E   K   ++ EK  E++RQ +KL  +YD LR   
Sbjct:   185 TQQIQSKDVELTSMKGEVTSMKKVLEEYKKKFSDISEKLMERNRQYQKLQGLYDSLRLRN 244

Query:   176 ESM--KRSAIQPS 186
              S+  + S ++PS
Sbjct:   245 ISIANQESTLEPS 257

GO:0051026 "chiasma assembly" evidence=IEA

GO:0035265 "organ growth" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0007132 "meiotic metaphase I" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0001825 "blastocyst formation" evidence=IEA

UNIPROTKB|G3V5S3 CCNB1IP1 "E3 ubiquitin-protein ligase CCNB1IP1" [Homo sapiens (taxid:9606)]

 Score = 144 (55.7 bits), Expect = 1.3e-09, P = 1.3e-09
 Identities = 36/146 (24%), Positives = 73/146 (50%)

Query:     3 CN--ACWRELEGRAISTTCGHLLCTEDANKILSNDAA-CPICDQVLSKSL-MKPVDINPN 58
             CN   C  +L G A  T C H+ C +  +   S   A CP C+  LS  L +   +++P+
Sbjct:    10 CNYRKCRIKLSGYAWVTACSHIFCDQHGSGEFSRSPAICPACNSTLSGKLDIVRTELSPS 69

Query:    59 DEWVNMAMAGVSPQILMKSAYRSVMFY---LGQKELEMQYKMNRIVAQCRQKCEAMQEKF 115
             +E+  M +AG+ P+I++  + R++ F+   + Q+ L  +Y  ++     +Q    M++ +
Sbjct:    70 EEYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSKAEGHLKQ----MEKIY 125

Query:   116 TEKLEQVHTAYQKMAKRCQMMEQEIE 141
             T++++        M      M++ +E
Sbjct:   126 TQQIQSKDVELTSMKGEVTSMKKVLE 151

GO:0001825 "blastocyst formation" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0007132 "meiotic metaphase I" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0035265 "organ growth" evidence=IEA

GO:0051026 "chiasma assembly" evidence=IEA

UNIPROTKB|E1BV34 Gga.3145 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 116 (45.9 bits), Expect = 0.00069, P = 0.00069
 Identities = 34/131 (25%), Positives = 65/131 (49%)

Query:    47 KSLMKPVDINPNDEWVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQ 106
             K ++KP+D    D +V  A     P++ +    R +   +G  EL M+ +    +   + 
Sbjct:   254 KFVIKPIDKKAPD-FVFYA-----PRLRINK--RILALCMGNHELYMRRRKPDTIEVQQM 305

Query:   107 KCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLD- 165
             K +A +EK  +++E V    +   K+ ++ E+E E + ++K+EL EK  +   Q +K   
Sbjct:   306 KAQAREEKHQKQMESVRALLENEKKKRELAEKEKEKIEREKEELMEKLKQIEEQTKKAQQ 365

Query:   166 EMYDQLRSEYE 176
             E+ +Q R   E
Sbjct:   366 ELEEQTRRAME 376


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        0.316   0.130   0.387    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      302       302   0.00097  115 3  11 22  0.41    34
                                                     33  0.45    37


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:  9
  No. of states in DFA:  608 (65 KB)
  Total size of DFA:  226 KB (2124 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:  44.61u 0.12s 44.73t   Elapsed:  00:00:02
  Total cpu time:  44.61u 0.12s 44.73t   Elapsed:  00:00:02
  Start:  Sat May 11 06:56:00 2013   End:  Sat May 11 06:56:02 2013

GO:0005856 "cytoskeleton" evidence=IEA

GO:0008092 "cytoskeletal protein binding" evidence=IEA

GO:0019898 "extrinsic to membrane" evidence=IEA

GO:0001931 "uropod" evidence=IEA

GO:0005102 "receptor binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005902 "microvillus" evidence=IEA

GO:0005925 "focal adhesion" evidence=IEA

GO:0007159 "leukocyte cell-cell adhesion" evidence=IEA

GO:0016323 "basolateral plasma membrane" evidence=IEA

GO:0016324 "apical plasma membrane" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0022614 "membrane to membrane docking" evidence=IEA

GO:0030175 "filopodium" evidence=IEA

GO:0050839 "cell adhesion molecule binding" evidence=IEA

GO:0050900 "leukocyte migration" evidence=IEA

GO:2000401 "regulation of lymphocyte migration" evidence=IEA

---

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: eugene3.01680006 hypothetical protein (301 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	302
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-06
pfam10158	131	pfam10158, LOH1CR12, Tumour suppressor protein	1e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-04
cd07657	237	cd07657, F-BAR_Fes_Fer, The F-BAR (FES-CIP4 Homolo	0.002
pfam04111	356	pfam04111, APG6, Autophagy protein Apg6	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003

>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 14/41 (34%), Positives = 18/41 (43%)

Query: 3  CNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQ 43
          C  C   L    + T CGH+ C E   + L   + CPIC  
Sbjct: 5  CPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

>gnl|CDD|118686 pfam10158, LOH1CR12, Tumour suppressor protein

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 17/68 (25%), Positives = 34/68 (50%)

Query: 106 QKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLD 165
             C  +QE   +  E V +    + KR + ++  I +L  +  E Q++++  + Q  K++
Sbjct: 31  NLCTRLQEHLNQCAEAVASDQNALVKRIKEVDASIITLFAEMVERQKRYASYAEQFSKVN 90

Query: 166 EMYDQLRS 173
           E+  QLR 
Sbjct: 91  EISAQLRR 98

This is a region of 130 amino acids that is the most conserved region of hypothetical proteins involved in loss of heterozygosity and thus tumour suppression. The exact function is not known. Length = 131

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

 Score = 40.9 bits (96), Expect = 8e-04
 Identities = 20/96 (20%), Positives = 52/96 (54%), Gaps = 4/96 (4%)

Query: 89  KELEMQYKMNRI----VAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLS 144
           +ELE + +        + +  +  E  +E+  +++E++    +++ ++   +E+E+E L 
Sbjct: 796 EELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELE 855

Query: 145 KDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
           K+ +EL+E+  E   +K +L++   +L  E E ++ 
Sbjct: 856 KELEELKEELEELEAEKEELEDELKELEEEKEELEE 891

Length = 1163

>gnl|CDD|153341 cd07657, F-BAR_Fes_Fer, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and Fer (Fes related) tyrosine kinases

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 5/87 (5%)

Query: 91  LEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEI-ESLSKDKQE 149
            E+    +++    +Q  EA++    +KL  +    +K  K  Q   Q+I E   K   E
Sbjct: 68  KEIMDSTDQLSKLIKQHAEALESGTLDKLTLLIKDKRKAKKAYQEERQQIDEQYKKLTDE 127

Query: 150 LQEKFSEKSRQKRKLDEMYDQLRSEYE 176
           +++  SE     +KL E Y   +S++E
Sbjct: 128 VEKLKSE----YQKLLEDYKAAKSKFE 150

F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Fes (feline sarcoma), also called Fps (Fujinami poultry sarcoma), and Fer (Fes related) are cytoplasmic (or nonreceptor) tyrosine kinases that play roles in haematopoiesis, inflammation and immunity, growth factor signaling, cytoskeletal regulation, cell migration and adhesion, and the regulation of cell-cell interactions. Although Fes and Fer show redundancy in their biological functions, they show differences in their expression patterns. Fer is ubiquitously expressed while Fes is expressed predominantly in myeloid and endothelial cells. Fes and Fer contain an N-terminal F-BAR domain, an SH2 domain, and a C-terminal catalytic kinase domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. The F-BAR domain of Fes is critical in its role in microtubule nucleation and bundling. Length = 237

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

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 21/96 (21%), Positives = 38/96 (39%), Gaps = 1/96 (1%)

Query: 89  KELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQ 148
            EL    K      Q   K E+   +     E + +   ++ K  + +  E+E L K+  
Sbjct: 36  SELRDAEKERDTYKQYLSKLESQNVE-ISNYEALDSELDELKKEEERLLDELEELEKEDD 94

Query: 149 ELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSAIQ 184
           +L  +  E   +K +L+    Q   EY    R+ +Q
Sbjct: 95  DLDGELVELQEEKEQLENEELQYLREYNLFDRNNLQ 130

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

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

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 3/61 (4%)

Query: 117 EKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE 176
           E+LE+   + ++   +   +++EIE L + +Q LQE+  E   +  + +   D L  E E
Sbjct: 761 EELEEELESLEEALAK---LKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELE 817

Query: 177 S 177
           S
Sbjct: 818 S 818

Length = 1163

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	302
KOG4739	233	consensus Uncharacterized protein involved in syna	99.3
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.15
PF14634	44	zf-RING_5: zinc-RING finger domain	99.08
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.07
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.06
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.94
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.91
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.9
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.83
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.69
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.68
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.67
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.62
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.6
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.55
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.52
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.46
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.43
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.4
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.3
KOG3039	303	consensus Uncharacterized conserved protein [Funct	98.28
COG5152	259	Uncharacterized conserved protein, contains RING a	98.12
PF04641	260	Rtf2: Rtf2 RING-finger	98.12
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.09
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.08
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	98.07
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.03
COG5222	427	Uncharacterized conserved protein, contains RING Z	97.84
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	97.58
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.57
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.56
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.54
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.51
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.4
KOG2660	331	consensus Locus-specific chromosome binding protei	97.34
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	97.22
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.16
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	97.13
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	97.05
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.9
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.89
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	96.83
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	96.81
KOG0825	1134	consensus PHD Zn-finger protein [General function	96.78
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	96.75
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.65
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.61
PHA02926	242	zinc finger-like protein; Provisional	96.6
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.44
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.25
PF10186	302	Atg14: UV radiation resistance protein and autopha	96.2
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	96.0
PHA02562	562	46 endonuclease subunit; Provisional	95.93
KOG3113	293	consensus Uncharacterized conserved protein [Funct	95.59
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	95.38
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	95.37
PRK11637	428	AmiB activator; Provisional	95.35
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	95.31
PF09738	302	DUF2051: Double stranded RNA binding protein (DUF2	95.3
PF05010	207	TACC: Transforming acidic coiled-coil-containing p	95.28
PRK11637	428	AmiB activator; Provisional	95.25
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	95.24
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	95.21
KOG1962	216	consensus B-cell receptor-associated protein and r	95.11
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	95.1
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	95.05
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	94.99
PRK10884	206	SH3 domain-containing protein; Provisional	94.86
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	94.51
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	94.3
PF04949	159	Transcrip_act: Transcriptional activator; InterPro	94.12
KOG1941	518	consensus Acetylcholine receptor-associated protei	93.96
PRK02224	880	chromosome segregation protein; Provisional	93.79
PRK10884	206	SH3 domain-containing protein; Provisional	93.49
PF06120	301	Phage_HK97_TLTM: Tail length tape measure protein;	93.49
PF04899	70	MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 Th	93.42
PRK15422	79	septal ring assembly protein ZapB; Provisional	93.2
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	93.18
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	93.03
KOG1962	216	consensus B-cell receptor-associated protein and r	92.73
PF12709	87	Kinetocho_Slk19: Central kinetochore-associated; I	92.71
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	92.66
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	92.62
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	92.58
KOG4001	259	consensus Axonemal dynein light chain [Cytoskeleto	92.51
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	92.38
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.37
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	92.36
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	92.02
PF10498	359	IFT57: Intra-flagellar transport protein 57 ; Inte	92.0
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	91.91
KOG0946	970	consensus ER-Golgi vesicle-tethering protein p115	91.91
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	91.87
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	91.65
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	91.59
KOG4367	699	consensus Predicted Zn-finger protein [Function un	91.52
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	91.41
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	91.38
PRK10780	165	periplasmic chaperone; Provisional	91.34
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	91.33
COG2433	652	Uncharacterized conserved protein [Function unknow	91.29
PF00038	312	Filament: Intermediate filament protein; InterPro:	91.09
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	91.08
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	91.04
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	90.96
PF12777	344	MT: Microtubule-binding stalk of dynein motor; Int	90.89
COG5175	480	MOT2 Transcriptional repressor [Transcription]	90.89
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	90.75
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	90.75
PRK00409	782	recombination and DNA strand exchange inhibitor pr	90.64
PRK12775	1006	putative trifunctional 2-polyprenylphenol hydroxyl	90.63
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	90.58
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	90.53
COG5236	493	Uncharacterized conserved protein, contains RING Z	90.39
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	90.11
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	90.0
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	89.91
COG2433	652	Uncharacterized conserved protein [Function unknow	89.85
COG4026	290	Uncharacterized protein containing TOPRIM domain,	89.85
TIGR02680	1353	conserved hypothetical protein TIGR02680. Members	89.81
PRK13169	110	DNA replication intiation control protein YabA; Re	89.68
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	89.64
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	89.57
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	89.56
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	89.48
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	89.44
PF15290	305	Syntaphilin: Golgi-localised syntaxin-1-binding cl	89.37
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	89.35
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	89.33
PF07889	126	DUF1664: Protein of unknown function (DUF1664); In	89.28
PHA03096	284	p28-like protein; Provisional	89.17
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	88.95
PF10481	307	CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR0	88.82
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	88.8
PHA02562	562	46 endonuclease subunit; Provisional	88.77
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	88.69
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	88.63
KOG1850	391	consensus Myosin-like coiled-coil protein [Cytoske	88.51
PRK04325	74	hypothetical protein; Provisional	88.46
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	88.45
KOG0243	1041	consensus Kinesin-like protein [Cytoskeleton]	88.19
KOG3002	299	consensus Zn finger protein [General function pred	88.05
PF03938	158	OmpH: Outer membrane protein (OmpH-like); InterPro	87.98
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	87.73
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	87.54
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	87.42
KOG3859	406	consensus Septins (P-loop GTPases) [Cell cycle con	87.38
KOG1853	333	consensus LIS1-interacting protein NUDE [Cytoskele	87.35
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	87.35
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	87.33
COG0419	908	SbcC ATPase involved in DNA repair [DNA replicatio	87.3
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	87.24
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	87.17
PF10498	359	IFT57: Intra-flagellar transport protein 57 ; Inte	87.02
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	87.02
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	87.0
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	86.94
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	86.9
PF09728	309	Taxilin: Myosin-like coiled-coil protein; InterPro	86.88
PF03148	384	Tektin: Tektin family; InterPro: IPR000435 Tektin	86.86
PRK02119	73	hypothetical protein; Provisional	86.84
PF10205	102	KLRAQ: Predicted coiled-coil domain-containing pro	86.83
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	86.78
PRK09039	343	hypothetical protein; Validated	86.7
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	86.52
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	86.45
COG4372	499	Uncharacterized protein conserved in bacteria with	86.44
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	86.43
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	86.35
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	86.26
PF10186	302	Atg14: UV radiation resistance protein and autopha	86.24
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	86.11
PF08581	79	Tup_N: Tup N-terminal; InterPro: IPR013890 The N-t	86.03
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	86.01
PRK02793	72	phi X174 lysis protein; Provisional	85.96
PF12777	344	MT: Microtubule-binding stalk of dynein motor; Int	85.8
PF10392	132	COG5: Golgi transport complex subunit 5; InterPro:	85.73
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	85.69
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	85.61
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	85.6
PRK02224	880	chromosome segregation protein; Provisional	85.45
KOG4367	699	consensus Predicted Zn-finger protein [Function un	85.19
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	85.18
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	85.16
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	85.01
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	84.96
KOG3647	338	consensus Predicted coiled-coil protein [General f	84.93
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	84.84
PRK11546	143	zraP zinc resistance protein; Provisional	84.71
PF10158	131	LOH1CR12: Tumour suppressor protein; InterPro: IPR	84.7
PRK04406	75	hypothetical protein; Provisional	84.62
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	84.53
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	84.47
PRK00409	782	recombination and DNA strand exchange inhibitor pr	84.46
PF13942	179	Lipoprotein_20: YfhG lipoprotein	84.44
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	84.37
TIGR01005	754	eps_transp_fam exopolysaccharide transport protein	84.33
PRK09841	726	cryptic autophosphorylating protein tyrosine kinas	84.3
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	84.16
PHA01750	75	hypothetical protein	83.72
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	83.63
PRK12704	520	phosphodiesterase; Provisional	83.63
PRK00846	77	hypothetical protein; Provisional	83.6
TIGR01010	362	BexC_CtrB_KpsE polysaccharide export inner-membran	83.52
PRK10920	390	putative uroporphyrinogen III C-methyltransferase;	83.52
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	83.34
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	83.34
PF07544	83	Med9: RNA polymerase II transcription mediator com	83.33
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	83.31
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	83.25
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	83.23
PF09738	302	DUF2051: Double stranded RNA binding protein (DUF2	83.21
COG2900	72	SlyX Uncharacterized protein conserved in bacteria	83.21
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	83.11
PF15254	861	CCDC14: Coiled-coil domain-containing protein 14	82.98
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	82.89
PF00038	312	Filament: Intermediate filament protein; InterPro:	82.82
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	82.8
KOG4466	291	consensus Component of histone deacetylase complex	82.68
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	82.66
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	82.65
KOG2129	552	consensus Uncharacterized conserved protein H4 [Fu	82.6
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	82.48
KOG4848	225	consensus Extracellular matrix-associated peroxida	82.47
KOG4657	246	consensus Uncharacterized conserved protein [Funct	82.45
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	82.38
PRK11519	719	tyrosine kinase; Provisional	82.38
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	82.24
PRK00888	105	ftsB cell division protein FtsB; Reviewed	82.11
PRK01156	895	chromosome segregation protein; Provisional	81.93
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	81.82
COG4026	290	Uncharacterized protein containing TOPRIM domain,	81.71
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	81.67
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	81.63
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	81.62
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	81.47
KOG4571	294	consensus Activating transcription factor 4 [Trans	81.26
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	81.18
KOG1850	391	consensus Myosin-like coiled-coil protein [Cytoske	81.14
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	81.05
PF10212	518	TTKRSYEDQ: Predicted coiled-coil domain-containing	81.04
KOG0709	472	consensus CREB/ATF family transcription factor [Tr	81.03
PRK09039	343	hypothetical protein; Validated	80.99
COG0497	557	RecN ATPase involved in DNA repair [DNA replicatio	80.93
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	80.54
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	80.47
PRK03918	880	chromosome segregation protein; Provisional	80.4
PF12240	205	Angiomotin_C: Angiomotin C terminal; InterPro: IPR	80.33
KOG4460	741	consensus Nuclear pore complex, Nup88/rNup84 compo	80.21
cd07656	241	F-BAR_srGAP The F-BAR (FES-CIP4 Homology and Bin/A	80.17
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	80.13
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	80.1
KOG0289	506	consensus mRNA splicing factor [General function p	80.06
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	80.06

>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=99.30  E-value=7.4e-11  Score=108.64  Aligned_cols=148  Identities=18%  Similarity=0.325  Sum_probs=83.5

Q ss_pred             CccccCccccc-CCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcccccCCChHHHHHHhcCCChHHHHHHHH
Q 022126            1 MRCNACWRELE-GRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDEWVNMAMAGVSPQILMKSAY   79 (302)
Q Consensus         1 l~CNiC~~~l~-~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~~LnPse~~Kt~vL~GlsP~~Ime~a~   79 (302)
                      .+||.|+..-. +..++|.|+||||..|....  ....||.|++++..     +.|+++-..-...+++..|..|-++..
T Consensus         4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~ir~-----i~l~~slp~~ik~~F~d~~~~~~~~~~   76 (233)
T KOG4739|consen    4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSIRI-----IQLNRSLPTDIKSYFADPPRLIQDLYR   76 (233)
T ss_pred             EEeccccccCCCCceeeeechhhhhhhhcccC--Cccccccccceeee-----eecccccchhHHHHccCcHHHHHHHHH
Confidence            48999997654 46789999999999997664  23499999998543     233333221224567767765555544


Q ss_pred             ---HhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 022126           80 ---RSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSE  156 (302)
Q Consensus        80 ---RAi~Fw~~Q~~qe~~yQ~~~l~~~lreK~e~L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~E  156 (302)
                         +.++|+..|..+...++.    +++. +-....+.+.+|..+.+.++.+              ++..+++...+|+.
T Consensus        77 ~l~r~i~fq~~qr~~~~~~~~----~~~~-~~req~~~~~~K~~e~~~ql~k--------------e~a~~~~nrk~~~~  137 (233)
T KOG4739|consen   77 KLQRVINFQHKQRNLQVKLEL----KQLE-KDREQTAYFEKKTQEETQQLSK--------------EEAFIENNRKKLQA  137 (233)
T ss_pred             HHHHHHhhHHHHHHHHHHHHH----HHHH-HHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHH
Confidence               455555555543333321    1111 1122333444444444443332              34444555556666


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 022126          157 KSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       157 KsRq~~qLqelYdkLK~~  174 (302)
                      ..++.++++.+...+...
T Consensus       138 ~E~~nrka~~~~~~~e~~  155 (233)
T KOG4739|consen  138 SELENRKAERLISALELK  155 (233)
T ss_pred             HHHHHHHHHhchhhhhhc
Confidence            667777777666554433

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.15  E-value=1.4e-11  Score=112.78  Aligned_cols=53  Identities=30%  Similarity=0.653  Sum_probs=46.1

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc---CCCCCCCCccccccCCCcccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS---NDAACPICDQVLSKSLMKPVD   54 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~---~~~~CPvC~~~l~~~div~~~   54 (302)
                      |-||||.+.- .+||||-|||.||+-|+.+|+.   +...||+|+...+.+.||++.
T Consensus        48 FdCNICLd~a-kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlY  103 (230)
T KOG0823|consen   48 FDCNICLDLA-KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLY  103 (230)
T ss_pred             eeeeeecccc-CCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeee
Confidence            5699999875 4799999999999999999975   467899999999988888853

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.08  E-value=7.9e-11  Score=81.70  Aligned_cols=42  Identities=33%  Similarity=0.908  Sum_probs=37.7

Q ss_pred             ccccCccccc--CCcEEecCCccccHHHHHhhhcCCCCCCCCcc
Q 022126            2 RCNACWRELE--GRAISTTCGHLLCTEDANKILSNDAACPICDQ   43 (302)
Q Consensus         2 ~CNiC~~~l~--~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~   43 (302)
                      +||+|++.+.  ..+++|+|||+||..|+.+.......||+|++
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            6999999993  47999999999999999999766889999985

>smart00504 Ubox Modified RING finger domain

Probab=99.07  E-value=1.1e-10  Score=85.34  Aligned_cols=51  Identities=16%  Similarity=0.257  Sum_probs=45.9

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~   52 (302)
                      |.|++|.+.+. +||++.|||+||..|+.+++.....||+|+..++..++++
T Consensus         2 ~~Cpi~~~~~~-~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~   52 (63)
T smart00504        2 FLCPISLEVMK-DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIP   52 (63)
T ss_pred             cCCcCCCCcCC-CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhcee
Confidence            67999999986 5999999999999999999988889999999998777655

Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.06  E-value=8.6e-11  Score=105.59  Aligned_cols=52  Identities=29%  Similarity=0.737  Sum_probs=43.9

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc----------------CCCCCCCCccccccCCCccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS----------------NDAACPICDQVLSKSLMKPV   53 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~----------------~~~~CPvC~~~l~~~div~~   53 (302)
                      +.|+||.+.+. ++|+|.|||+||+.||.+|+.                ....||+|++.++..+++++
T Consensus        19 ~~CpICld~~~-dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPi   86 (193)
T PLN03208         19 FDCNICLDQVR-DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPI   86 (193)
T ss_pred             cCCccCCCcCC-CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEe
Confidence            57999999885 699999999999999999863                13589999999988776654

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A

Probab=98.94  E-value=4.8e-10  Score=75.66  Aligned_cols=38  Identities=39%  Similarity=0.989  Sum_probs=33.0

Q ss_pred             cccCcccccCCc-EEecCCccccHHHHHhhhcCCCCCCCC
Q 022126            3 CNACWRELEGRA-ISTTCGHLLCTEDANKILSNDAACPIC   41 (302)
Q Consensus         3 CNiC~~~l~~~~-vvT~CGHiFC~~Ci~~~~~~~~~CPvC   41 (302)
                      |+||.+.+.+ + +++.|||+||..|+.++++....||+|
T Consensus         1 C~iC~~~~~~-~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD-PVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS-EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC-cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            8999998875 6 799999999999999999888899998

>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A

Probab=98.91  E-value=8.7e-10  Score=76.20  Aligned_cols=38  Identities=26%  Similarity=0.784  Sum_probs=29.8

Q ss_pred             cccCcccccCCcEEecCCccccHHHHHhhhcC----CCCCCCC
Q 022126            3 CNACWRELEGRAISTTCGHLLCTEDANKILSN----DAACPIC   41 (302)
Q Consensus         3 CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~----~~~CPvC   41 (302)
                      |+||.+.|+ +||++.|||+||..|+.++|+.    ...||.|
T Consensus         1 CpiC~~~~~-~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFK-DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-S-SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhC-CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            899999996 6999999999999999999874    2579998

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.90  E-value=6.2e-08  Score=92.82  Aligned_cols=49  Identities=27%  Similarity=0.655  Sum_probs=39.3

Q ss_pred             ccccCccc--ccC--CcEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCC
Q 022126            2 RCNACWRE--LEG--RAISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLM   50 (302)
Q Consensus         2 ~CNiC~~~--l~~--~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~di   50 (302)
                      .|++|...  ++.  ..++..|||.||..|+..+|.. ...||+|++.+....+
T Consensus         5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~f   58 (309)
T TIGR00570         5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNF   58 (309)
T ss_pred             CCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhc
Confidence            69999985  332  2456689999999999999865 6689999999987654

All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A

Probab=98.83  E-value=1.9e-09  Score=74.34  Aligned_cols=41  Identities=27%  Similarity=0.798  Sum_probs=36.3

Q ss_pred             ccccCccccc--CCcEEecCCccccHHHHHhhhcCCCCCCCCc
Q 022126            2 RCNACWRELE--GRAISTTCGHLLCTEDANKILSNDAACPICD   42 (302)
Q Consensus         2 ~CNiC~~~l~--~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~   42 (302)
                      .|+||...+.  +.++++.|||+||..|+..|+....+||+|+
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            4999999995  4788999999999999999998888999996

...

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.69  E-value=8e-09  Score=102.05  Aligned_cols=47  Identities=30%  Similarity=0.704  Sum_probs=41.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKS   48 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~   48 (302)
                      |.|+||...+. .||+|.|||.||..|+..++.....||+|+..+...
T Consensus        27 l~C~IC~d~~~-~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        27 LRCHICKDFFD-VPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             cCCCcCchhhh-CccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            58999999885 689999999999999999998877899999987643

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

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=98.68  E-value=1.9e-08  Score=71.23  Aligned_cols=45  Identities=33%  Similarity=0.854  Sum_probs=39.2

Q ss_pred             CccccCcccccCCcEEecCCcc-ccHHHHHhhhcCCCCCCCCccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHL-LCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHi-FC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      ..|.+|++... .+++..|||. ||..|+.+++.....||+|+++++
T Consensus         3 ~~C~iC~~~~~-~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    3 EECPICFENPR-DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             SB-TTTSSSBS-SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             CCCccCCccCC-ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            36999999875 6999999999 999999999999999999999875

...

>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

Probab=98.67  E-value=1.8e-08  Score=67.15  Aligned_cols=44  Identities=27%  Similarity=0.791  Sum_probs=36.2

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhcC-CCCCCCCcccc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILSN-DAACPICDQVL   45 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l   45 (302)
                      .|++|...+....+++.|||.||..|+..++.. ...||.|+..+
T Consensus         1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            489999998544445559999999999999886 77899999753

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.62  E-value=2.2e-08  Score=67.67  Aligned_cols=38  Identities=32%  Similarity=0.875  Sum_probs=33.8

Q ss_pred             cccCcccccCCcE-EecCCccccHHHHHhhhc--CCCCCCCC
Q 022126            3 CNACWRELEGRAI-STTCGHLLCTEDANKILS--NDAACPIC   41 (302)
Q Consensus         3 CNiC~~~l~~~~v-vT~CGHiFC~~Ci~~~~~--~~~~CPvC   41 (302)
                      |+||...+.. ++ ++.|||.||..|+.++++  ....||.|
T Consensus         1 C~iC~~~~~~-~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFED-PVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSS-EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccC-CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            8999998864 55 999999999999999988  57789998

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. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.60  E-value=1.9e-08  Score=101.08  Aligned_cols=52  Identities=27%  Similarity=0.675  Sum_probs=44.5

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-----CCCCCCCccccccCCCccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-----DAACPICDQVLSKSLMKPV   53 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-----~~~CPvC~~~l~~~div~~   53 (302)
                      +.|+||+.+.. -|+.|.|||+||..||.++|.-     -..||+|+..++.+|+.++
T Consensus       187 ~~CPICL~~~~-~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv  243 (513)
T KOG2164|consen  187 MQCPICLEPPS-VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPV  243 (513)
T ss_pred             CcCCcccCCCC-cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeee
Confidence            47999999875 6999999999999999999853     4689999999998776554

>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis

Probab=98.55  E-value=5.4e-08  Score=74.40  Aligned_cols=51  Identities=20%  Similarity=0.264  Sum_probs=41.6

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~div~   52 (302)
                      |.|+||+..+. +||++.|||+|+..||.+|+.. ...||.|+..++..++++
T Consensus         5 f~CpIt~~lM~-dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~p   56 (73)
T PF04564_consen    5 FLCPITGELMR-DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIP   56 (73)
T ss_dssp             GB-TTTSSB-S-SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE
T ss_pred             cCCcCcCcHhh-CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceE
Confidence            68999999986 6999999999999999999987 899999999998877655

Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B

Probab=98.52  E-value=2.6e-08  Score=74.93  Aligned_cols=47  Identities=21%  Similarity=0.674  Sum_probs=25.4

Q ss_pred             CccccCcccccCCcE-EecCCccccHHHHHhhhcCCCCCCCCccccccCCC
Q 022126            1 MRCNACWRELEGRAI-STTCGHLLCTEDANKILSNDAACPICDQVLSKSLM   50 (302)
Q Consensus         1 l~CNiC~~~l~~~~v-vT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~di   50 (302)
                      |+|++|...|+ .|| ++.|.|+||..|+...+.  ..||+|+++-...|+
T Consensus         8 LrCs~C~~~l~-~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~   55 (65)
T PF14835_consen    8 LRCSICFDILK-EPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDI   55 (65)
T ss_dssp             TS-SSS-S--S-S-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS-
T ss_pred             cCCcHHHHHhc-CCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHH
Confidence            68999999986 465 799999999999988754  359999999877776

>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]

Probab=98.46  E-value=4.8e-08  Score=94.20  Aligned_cols=49  Identities=29%  Similarity=0.687  Sum_probs=44.9

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLM   50 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~di   50 (302)
                      |+|-||+..|. -|++|+|||.||.-||.+++.....||.|...+++.++
T Consensus        24 LRC~IC~eyf~-ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~L   72 (442)
T KOG0287|consen   24 LRCGICFEYFN-IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDL   72 (442)
T ss_pred             HHHhHHHHHhc-CceeccccchHHHHHHHHHhccCCCCCceecccchhhh
Confidence            58999999886 69999999999999999999999999999999887654

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

Probab=98.43  E-value=8.5e-08  Score=90.92  Aligned_cols=46  Identities=28%  Similarity=0.687  Sum_probs=41.5

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      ++|-||...|+ -+++|+|||.||.-||..++.....||+|+....+
T Consensus        26 lrC~IC~~~i~-ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          26 LRCRICDCRIS-IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             HHhhhhhheee-cceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence            47999999886 59999999999999999999999999999987643

>smart00184 RING Ring finger

Probab=98.40  E-value=2.7e-07  Score=59.26  Aligned_cols=38  Identities=37%  Similarity=0.912  Sum_probs=33.2

Q ss_pred             cccCcccccCCcEEecCCccccHHHHHhhhc-CCCCCCCC
Q 022126            3 CNACWRELEGRAISTTCGHLLCTEDANKILS-NDAACPIC   41 (302)
Q Consensus         3 CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~-~~~~CPvC   41 (302)
                      |++|.... ..++++.|||+||..|+..++. ....||+|
T Consensus         1 C~iC~~~~-~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL-KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC-CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            78999885 4688999999999999999987 56779988

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A

Probab=98.30  E-value=3.6e-07  Score=63.69  Aligned_cols=36  Identities=25%  Similarity=0.726  Sum_probs=21.6

Q ss_pred             cccCcccccC---CcEEecCCccccHHHHHhhhcC----CCCCC
Q 022126            3 CNACWRELEG---RAISTTCGHLLCTEDANKILSN----DAACP   39 (302)
Q Consensus         3 CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~~~----~~~CP   39 (302)
                      |+||++ +.+   .|++..|||+||++|+.++++.    ...||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899998 642   4899999999999999999763    45676

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.28  E-value=4.1e-07  Score=84.59  Aligned_cols=54  Identities=20%  Similarity=0.342  Sum_probs=49.8

Q ss_pred             CccccCcccccC---CcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcccc
Q 022126            1 MRCNACWRELEG---RAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVD   54 (302)
Q Consensus         1 l~CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~~   54 (302)
                      +.|++|+..|++   .+|+..|||+||.+|..++...++.||+|+++++++|||.+.
T Consensus       222 yiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~Lq  278 (303)
T KOG3039|consen  222 YICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQ  278 (303)
T ss_pred             eecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeee
Confidence            479999999974   588999999999999999999999999999999999998865

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=98.12  E-value=6.3e-07  Score=81.18  Aligned_cols=46  Identities=24%  Similarity=0.624  Sum_probs=41.5

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      |.|-||.+.+. .||+|.|||.||..|+.+-+.....|-+|++....
T Consensus       197 F~C~iCKkdy~-spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G  242 (259)
T COG5152         197 FLCGICKKDYE-SPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG  242 (259)
T ss_pred             eeehhchhhcc-chhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence            67999999885 69999999999999999988889999999997654

>PF04641 Rtf2: Rtf2 RING-finger

Probab=98.12  E-value=1.6e-06  Score=81.23  Aligned_cols=57  Identities=21%  Similarity=0.589  Sum_probs=47.1

Q ss_pred             CccccCcccccC---CcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcccccCCChH
Q 022126            1 MRCNACWRELEG---RAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE   60 (302)
Q Consensus         1 l~CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~~LnPse~   60 (302)
                      |+||++...|++   -.++-+|||+|+..++...- ....||+|++++...|||+  |+|.++
T Consensus       114 ~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI~--Lnp~~e  173 (260)
T PF04641_consen  114 FICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDIIP--LNPPEE  173 (260)
T ss_pred             eECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEEE--ecCCcc
Confidence            589999999964   35577999999999999983 4678999999999999887  445544

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=98.09  E-value=3.5e-05  Score=76.86  Aligned_cols=43  Identities=23%  Similarity=0.584  Sum_probs=35.9

Q ss_pred             ccccCcccccC---CcEEecCCccccHHHHHhhhcCCCCCCCCccccc
Q 022126            2 RCNACWRELEG---RAISTTCGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      .|++|...+..   -.+.+-|.|.|=..|+.+|  ...+||+|+...+
T Consensus       177 TCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  177 TCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             CcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcC
Confidence            59999998863   3478889999999999999  4778999987665

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.08  E-value=2.9e-06  Score=65.08  Aligned_cols=41  Identities=27%  Similarity=0.716  Sum_probs=33.1

Q ss_pred             ccccCcccccC------------CcEEecCCccccHHHHHhhhcCCCCCCCCc
Q 022126            2 RCNACWRELEG------------RAISTTCGHLLCTEDANKILSNDAACPICD   42 (302)
Q Consensus         2 ~CNiC~~~l~~------------~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~   42 (302)
                      .|.||+..|.+            ..+...|||+|...||.+|++...+||+|+
T Consensus        21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            48899998821            235668999999999999999888999996

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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.07  E-value=1e-06  Score=83.68  Aligned_cols=46  Identities=28%  Similarity=0.624  Sum_probs=41.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      |.|-||++.+. .||+|.|||.||..|+.+.+.....|++|++....
T Consensus       242 f~c~icr~~f~-~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  242 FKCFICRKYFY-RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             ccccccccccc-cchhhcCCceeehhhhccccccCCcceeccccccc
Confidence            57999999996 69999999999999999999889999999997653

>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.03  E-value=1.9e-06  Score=76.43  Aligned_cols=42  Identities=21%  Similarity=0.695  Sum_probs=37.3

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQ   43 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~   43 (302)
                      +.|+||...+. .+++..|||.||..|+..++.....||.|+.
T Consensus        14 ~~C~iC~~~~~-~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   14 LTCPICLEYFR-EPVLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccChhhHHHhh-cCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            57999999997 4689999999999999999886678999993

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=97.84  E-value=1.1e-05  Score=77.00  Aligned_cols=43  Identities=33%  Similarity=0.785  Sum_probs=36.7

Q ss_pred             CccccCcccccCCcEEe-cCCccccHHHHHhhh-cCCCCCCCCccc
Q 022126            1 MRCNACWRELEGRAIST-TCGHLLCTEDANKIL-SNDAACPICDQV   44 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT-~CGHiFC~~Ci~~~~-~~~~~CPvC~~~   44 (302)
                      |.|+.|...+. .++-| .|||.||.+||...+ +.++.||.|.+.
T Consensus       275 LkCplc~~Llr-np~kT~cC~~~fc~eci~~al~dsDf~CpnC~rk  319 (427)
T COG5222         275 LKCPLCHCLLR-NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRK  319 (427)
T ss_pred             ccCcchhhhhh-CcccCccccchHHHHHHhhhhhhccccCCCcccc
Confidence            68999999886 57777 799999999999875 469999999883

>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.58  E-value=3.2e-05  Score=79.33  Aligned_cols=48  Identities=25%  Similarity=0.573  Sum_probs=41.2

Q ss_pred             ccccCcccccCC----cEEecCCccccHHHHHhhhcCCCCCCCCccccccCC
Q 022126            2 RCNACWRELEGR----AISTTCGHLLCTEDANKILSNDAACPICDQVLSKSL   49 (302)
Q Consensus         2 ~CNiC~~~l~~~----~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~d   49 (302)
                      .|.||++.+...    +-...|||+||..|+..|++...+||.|+..+....
T Consensus       293 ~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~~  344 (543)
T KOG0802|consen  293 LCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYDYV  344 (543)
T ss_pred             eeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhccc
Confidence            599999999743    678899999999999999999999999999554433

>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.57  E-value=2.7e-05  Score=74.31  Aligned_cols=45  Identities=20%  Similarity=0.484  Sum_probs=38.9

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhcCCCC-CCCCcccccc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILSNDAA-CPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~-CPvC~~~l~~   47 (302)
                      .|.||..... .||...|+|.||..||.....+++. |++|+.++..
T Consensus         9 eC~IC~nt~n-~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids   54 (324)
T KOG0824|consen    9 ECLICYNTGN-CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDS   54 (324)
T ss_pred             cceeeeccCC-cCccccccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence            4899998874 7899999999999999998777554 9999999865

>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.56  E-value=6.8e-05  Score=73.00  Aligned_cols=47  Identities=26%  Similarity=0.563  Sum_probs=40.2

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc-CCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS-NDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~-~~~~CPvC~~~l~~   47 (302)
                      +.|+||...|+....+.-|+|-||.+||.+.+. ....||.|++.|..
T Consensus        44 v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   44 VICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            579999999986566667999999999999875 47899999998854

>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.54  E-value=3.7e-05  Score=76.41  Aligned_cols=46  Identities=33%  Similarity=0.807  Sum_probs=41.3

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      |.|++|...|- .||+|.|||.||..|+.+.+.....||.|+..+..
T Consensus        85 f~c~vc~~~l~-~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   85 FECCVCSRALY-PPVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             hhhhhhHhhcC-CCccccccccccHHHHHHHhccCCCCccccccccc
Confidence            56999998885 69999999999999999988889999999998764

>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C

Probab=97.51  E-value=4.9e-05  Score=55.95  Aligned_cols=39  Identities=21%  Similarity=0.623  Sum_probs=28.1

Q ss_pred             CccccCcccccCCcEEe-cCCccccHHHHHhhhc--CCCCCCC
Q 022126            1 MRCNACWRELEGRAIST-TCGHLLCTEDANKILS--NDAACPI   40 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT-~CGHiFC~~Ci~~~~~--~~~~CPv   40 (302)
                      +.|+++...|. +||.. .|||+|.++.|..++.  ....||+
T Consensus        12 ~~CPiT~~~~~-~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   12 LKCPITLQPFE-DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             SB-TTTSSB-S-SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             cCCCCcCChhh-CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            58999999997 58765 8999999999999984  4678999

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.40  E-value=0.0016  Score=64.39  Aligned_cols=50  Identities=24%  Similarity=0.520  Sum_probs=36.9

Q ss_pred             ccccCccccc---CCcEEecCCccccHHHHHhhhcC--C-CCCCCCccccccCCCc
Q 022126            2 RCNACWRELE---GRAISTTCGHLLCTEDANKILSN--D-AACPICDQVLSKSLMK   51 (302)
Q Consensus         2 ~CNiC~~~l~---~~~vvT~CGHiFC~~Ci~~~~~~--~-~~CPvC~~~l~~~div   51 (302)
                      .|.||-+...   +-.-|.+|||+|-..|+.+||+.  . +.||+|+-.+....++
T Consensus         6 ~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~   61 (465)
T KOG0827|consen    6 ECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVA   61 (465)
T ss_pred             eeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeee
Confidence            5889954332   23447789999999999999984  3 6899999666655544

>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]

Probab=97.34  E-value=4.8e-05  Score=73.37  Aligned_cols=48  Identities=31%  Similarity=0.601  Sum_probs=42.9

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKS   48 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~   48 (302)
                      +.|..|...|.+...|+-|=|.||++||.++++....||.|+..+.+.
T Consensus        16 itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   16 ITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             eehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            469999999987777889999999999999999999999999987654

>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

Probab=97.22  E-value=0.00016  Score=71.09  Aligned_cols=45  Identities=27%  Similarity=0.614  Sum_probs=38.0

Q ss_pred             ccccCcccccC------------CcEEecCCccccHHHHHhhhcCCCCCCCCccccc
Q 022126            2 RCNACWRELEG------------RAISTTCGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~------------~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      .|-||++++-.            .|--.+|||+|-..|+..|+++..+||+|+.++-
T Consensus       289 ~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         289 TCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             eEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence            48899998421            3457789999999999999999999999999853

>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.16  E-value=0.0014  Score=65.00  Aligned_cols=49  Identities=29%  Similarity=0.636  Sum_probs=40.0

Q ss_pred             CccccCccccc----CCcEEecCCccccHHHHHhhhcC--CCCCCCCccccccCC
Q 022126            1 MRCNACWRELE----GRAISTTCGHLLCTEDANKILSN--DAACPICDQVLSKSL   49 (302)
Q Consensus         1 l~CNiC~~~l~----~~~vvT~CGHiFC~~Ci~~~~~~--~~~CPvC~~~l~~~d   49 (302)
                      +.|+||.+.+.    ...|+..|||.|=.+||.+|+..  .+.||.|...-++++
T Consensus         5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~   59 (463)
T KOG1645|consen    5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQ   59 (463)
T ss_pred             ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHH
Confidence            46999999875    25788999999999999999853  678999998765443

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.13  E-value=0.0054  Score=58.58  Aligned_cols=49  Identities=31%  Similarity=0.685  Sum_probs=39.6

Q ss_pred             ccccCccccc-C---CcEEecCCccccHHHHHhhhc-CCCCCCCCccccccCCC
Q 022126            2 RCNACWRELE-G---RAISTTCGHLLCTEDANKILS-NDAACPICDQVLSKSLM   50 (302)
Q Consensus         2 ~CNiC~~~l~-~---~~vvT~CGHiFC~~Ci~~~~~-~~~~CPvC~~~l~~~di   50 (302)
                      .|++|..... +   ...|-.|||..|.+|....|. ++..||.|.+.|.+..+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nf   55 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNF   55 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhccc
Confidence            5999886432 1   456779999999999999997 58899999999977554

>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.05  E-value=0.00028  Score=68.93  Aligned_cols=46  Identities=20%  Similarity=0.559  Sum_probs=39.1

Q ss_pred             ccccCccccc--CCcEEecCCccccHHHHHhhhcCC-CCCCCCcccccc
Q 022126            2 RCNACWRELE--GRAISTTCGHLLCTEDANKILSND-AACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~--~~~vvT~CGHiFC~~Ci~~~~~~~-~~CPvC~~~l~~   47 (302)
                      .|.||.+.+.  +.-.+.+|+|.|=..||+.|+... ..||+|+.....
T Consensus       231 ~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~  279 (348)
T KOG4628|consen  231 TCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT  279 (348)
T ss_pred             eEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence            5999999886  467799999999999999999865 559999996643

>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.90  E-value=0.0091  Score=56.27  Aligned_cols=45  Identities=29%  Similarity=0.713  Sum_probs=37.7

Q ss_pred             CccccCcccccC-----CcEEecCCccccHHHHHhhhcC-CCCCCCCcccc
Q 022126            1 MRCNACWRELEG-----RAISTTCGHLLCTEDANKILSN-DAACPICDQVL   45 (302)
Q Consensus         1 l~CNiC~~~l~~-----~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l   45 (302)
                      +.|+||...++.     .|-+..|||.||..|+.++..+ .-.||-|+...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            469999998862     4667779999999999999876 56799999985

>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]

Probab=96.89  E-value=0.0004  Score=68.88  Aligned_cols=50  Identities=34%  Similarity=0.693  Sum_probs=42.3

Q ss_pred             CccccCcccccCCcEE-ecCCccccHHHHHhhhcCCCCCCCCccccccCCCc
Q 022126            1 MRCNACWRELEGRAIS-TTCGHLLCTEDANKILSNDAACPICDQVLSKSLMK   51 (302)
Q Consensus         1 l~CNiC~~~l~~~~vv-T~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div   51 (302)
                      +.|++|...+. +|+. +.|||.||..|+..+......||+|...+.....+
T Consensus        22 l~C~~C~~vl~-~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~   72 (391)
T KOG0297|consen   22 LLCPICMSVLR-DPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL   72 (391)
T ss_pred             ccCcccccccc-CCCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence            46999999986 5777 59999999999999988899999999887665443

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=96.83  E-value=0.024  Score=53.19  Aligned_cols=47  Identities=30%  Similarity=0.709  Sum_probs=37.6

Q ss_pred             ccccCcccc--cC--CcEEec-CCccccHHHHHhhhcC-CCCCC--CCccccccC
Q 022126            2 RCNACWREL--EG--RAISTT-CGHLLCTEDANKILSN-DAACP--ICDQVLSKS   48 (302)
Q Consensus         2 ~CNiC~~~l--~~--~~vvT~-CGHiFC~~Ci~~~~~~-~~~CP--vC~~~l~~~   48 (302)
                      +|++|....  ..  ..+|.+ |=|-.|.+|..+.|+. ...||  -|++-|.+.
T Consensus        12 ~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~   66 (314)
T COG5220          12 RCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKI   66 (314)
T ss_pred             cCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHh
Confidence            699998653  21  345666 9999999999999985 77899  999988654

>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger

Probab=96.81  E-value=0.0013  Score=52.34  Aligned_cols=33  Identities=27%  Similarity=0.486  Sum_probs=28.0

Q ss_pred             cEEecCCccccHHHHHhhhcC---CCCCCCCccccc
Q 022126           14 AISTTCGHLLCTEDANKILSN---DAACPICDQVLS   46 (302)
Q Consensus        14 ~vvT~CGHiFC~~Ci~~~~~~---~~~CPvC~~~l~   46 (302)
                      .|.-.|||.|-..||.+|++.   ...||.|++...
T Consensus        47 lv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   47 LVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             eeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            356789999999999999874   578999999764

>KOG0825 consensus PHD Zn-finger protein [General function prediction only]

Probab=96.78  E-value=0.00041  Score=73.34  Aligned_cols=47  Identities=15%  Similarity=0.396  Sum_probs=37.2

Q ss_pred             ccccCcccccCCcE--EecCCccccHHHHHhhhcCCCCCCCCccccccC
Q 022126            2 RCNACWRELEGRAI--STTCGHLLCTEDANKILSNDAACPICDQVLSKS   48 (302)
Q Consensus         2 ~CNiC~~~l~~~~v--vT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~   48 (302)
                      .|++|...+.+.-+  -..|+|+||..|+..|-....+||+|+..|..-
T Consensus       125 ~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v  173 (1134)
T KOG0825|consen  125 QCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEV  173 (1134)
T ss_pred             hhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhee
Confidence            47788776654333  346999999999999988899999999998653

>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.75  E-value=0.00029  Score=51.85  Aligned_cols=44  Identities=25%  Similarity=0.734  Sum_probs=36.7

Q ss_pred             ccccCcccccCCcEEecCCcc-ccHHHHHhhhc-CCCCCCCCccccc
Q 022126            2 RCNACWRELEGRAISTTCGHL-LCTEDANKILS-NDAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHi-FC~~Ci~~~~~-~~~~CPvC~~~l~   46 (302)
                      .|.||.+... +.|+-+|||. +|.+|..+.+. ....||+|+.++.
T Consensus         9 ECTICye~pv-dsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    9 ECTICYEHPV-DSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ceeeeccCcc-hHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            4889998654 4778999997 59999999987 4789999999875

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=96.65  E-value=0.0007  Score=69.14  Aligned_cols=46  Identities=26%  Similarity=0.636  Sum_probs=38.0

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhc-----CCCCCCCCccccccC
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILS-----NDAACPICDQVLSKS   48 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~-----~~~~CPvC~~~l~~~   48 (302)
                      .|-+|.++- .++++++|-|.||..|+..+..     ...+||+|...|+-+
T Consensus       538 ~C~lc~d~a-ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  538 ECGLCHDPA-EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             eecccCChh-hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            588899875 4699999999999999977642     368999999988754

>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.61  E-value=0.00098  Score=66.21  Aligned_cols=44  Identities=20%  Similarity=0.440  Sum_probs=36.1

Q ss_pred             CccccCcccccC--CcEEecCCccccHHHHHhhhc--------CCCCCCCCccc
Q 022126            1 MRCNACWRELEG--RAISTTCGHLLCTEDANKILS--------NDAACPICDQV   44 (302)
Q Consensus         1 l~CNiC~~~l~~--~~vvT~CGHiFC~~Ci~~~~~--------~~~~CPvC~~~   44 (302)
                      +.|+||+....+  ..+.+.|+|+||..|+...++        ....||.|+-.
T Consensus       185 f~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~  238 (445)
T KOG1814|consen  185 FDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG  238 (445)
T ss_pred             ccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence            579999998765  678999999999999998864        25678887764

>PHA02926 zinc finger-like protein; Provisional

Probab=96.60  E-value=0.00097  Score=61.69  Aligned_cols=33  Identities=18%  Similarity=0.530  Sum_probs=26.9

Q ss_pred             ccccCcccccC--------CcEEecCCccccHHHHHhhhcC
Q 022126            2 RCNACWRELEG--------RAISTTCGHLLCTEDANKILSN   34 (302)
Q Consensus         2 ~CNiC~~~l~~--------~~vvT~CGHiFC~~Ci~~~~~~   34 (302)
                      .|.||++.+..        ..++..|+|+||..||.+|...
T Consensus       172 eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~  212 (242)
T PHA02926        172 ECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRT  212 (242)
T ss_pred             CCccCccccccccccccccccccCCCCchHHHHHHHHHHHh
Confidence            59999986521        3678899999999999999753

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=96.44  E-value=0.0011  Score=70.11  Aligned_cols=49  Identities=33%  Similarity=0.740  Sum_probs=41.1

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhcC--CCCCCCCccccccCCCcc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILSN--DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~--~~~CPvC~~~l~~~div~   52 (302)
                      -|.+|.. . +.+++|.|||.||.+|+...+..  ...||.|+..+...+++.
T Consensus       456 ~c~ic~~-~-~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s  506 (674)
T KOG1001|consen  456 WCHICCD-L-DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLS  506 (674)
T ss_pred             ccccccc-c-ccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhh
Confidence            5899998 4 57999999999999999998753  558999999997765544

>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.25  E-value=0.0022  Score=62.92  Aligned_cols=45  Identities=22%  Similarity=0.461  Sum_probs=39.9

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      .|+||...-. .+|.+.|||--|..||.+++-+...|--|++....
T Consensus       424 lCpICyA~pi-~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  424 LCPICYAGPI-NAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             cCcceecccc-hhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            4999987653 59999999999999999999999999999998753

>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=96.20  E-value=0.62  Score=43.14  Aligned_cols=20  Identities=20%  Similarity=0.632  Sum_probs=14.3

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHh
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANK   30 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~   30 (302)
                      .|++|.         +...+.+|..|+..
T Consensus         1 ~C~iC~---------~~~~~~~C~~C~~~   20 (302)
T PF10186_consen    1 QCPICH---------NSRRRFYCANCVNN   20 (302)
T ss_pred             CCCCCC---------CCCCCeECHHHHHH
Confidence            488888         34556778888766

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

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

Probab=96.00  E-value=0.14  Score=39.50  Aligned_cols=57  Identities=19%  Similarity=0.308  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          120 EQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       120 ~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +++++.|+++-.+++.++.|++.|+.+|.+|.+.-.+-..+..+|++-++..+.++.
T Consensus         7 ~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~   63 (72)
T PF06005_consen    7 EQLEEKIQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLR   63 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444555555566666677777777666665555555555555555555555543

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

>PHA02562 46 endonuclease subunit; Provisional

Probab=95.93  E-value=0.55  Score=47.70  Aligned_cols=14  Identities=36%  Similarity=0.926  Sum_probs=11.3

Q ss_pred             CCCCCCCCcccccc
Q 022126           34 NDAACPICDQVLSK   47 (302)
Q Consensus        34 ~~~~CPvC~~~l~~   47 (302)
                      ....||.|+..+..
T Consensus       283 ~~~~Cp~C~~~~~~  296 (562)
T PHA02562        283 KGGVCPTCTQQISE  296 (562)
T ss_pred             CCCCCCCCCCcCCC
Confidence            45699999998864

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.59  E-value=0.0079  Score=56.64  Aligned_cols=56  Identities=18%  Similarity=0.414  Sum_probs=45.6

Q ss_pred             CccccCcccccC---CcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcccccCCChH
Q 022126            1 MRCNACWRELEG---RAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPNDE   60 (302)
Q Consensus         1 l~CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~~LnPse~   60 (302)
                      |.|++-+-++++   -.++-.|||+|-..-+.++  ....|++|+..+...|+|++  ||.++
T Consensus       112 fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvIvl--Ng~~E  170 (293)
T KOG3113|consen  112 FICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVIVL--NGTEE  170 (293)
T ss_pred             eecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeEee--CCCHH
Confidence            579998888875   4668899999999888776  47899999999999998774  45544

>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]

Probab=95.38  E-value=0.0067  Score=60.38  Aligned_cols=47  Identities=26%  Similarity=0.559  Sum_probs=38.6

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhc--CCCCCCCCccccccCC
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILS--NDAACPICDQVLSKSL   49 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~--~~~~CPvC~~~l~~~d   49 (302)
                      .|-||-+.-+ +.-|-.|||..|..|+..|-.  ....||-|+-.+..-.
T Consensus       371 LCKICaendK-dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  371 LCKICAENDK-DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             HHHHhhccCC-CcccccccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            4888987654 567999999999999999864  3689999999987754

>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]

Probab=95.37  E-value=0.0065  Score=58.74  Aligned_cols=42  Identities=29%  Similarity=0.621  Sum_probs=33.1

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVL   45 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l   45 (302)
                      .|-.|...|.-.--...|-|+||.+|+.-.  .++.||.|...+
T Consensus        92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~--~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   92 FCDRCDFPIAIYGRMIPCKHVFCLECARSD--SDKICPLCDDRV  133 (389)
T ss_pred             eecccCCcceeeecccccchhhhhhhhhcC--ccccCcCcccHH
Confidence            377899888633447899999999998764  478999998754

>PRK11637 AmiB activator; Provisional

Probab=95.35  E-value=3.4  Score=41.23  Aligned_cols=42  Identities=17%  Similarity=0.211  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          133 CQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      ..+.+..++.|+++..+++..+.+..++..+|+.+...|+++
T Consensus       214 k~e~~~~l~~L~~~~~~~~~~l~~l~~~~~~L~~~I~~l~~~  255 (428)
T PRK11637        214 RNERKKTLTGLESSLQKDQQQLSELRANESRLRDSIARAERE  255 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344556666666777777777777777777777776543

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=95.31  E-value=0.37  Score=49.22  Aligned_cols=53  Identities=17%  Similarity=0.266  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          124 TAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       124 s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +++.+.+.|..++|++++.||++.+++.....+-.+++.+|+.-...|+.+++
T Consensus        69 SALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~  121 (475)
T PRK13729         69 HATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVK  121 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence            34555566777778888888777777777777777778888888888888854

>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=95.30  E-value=0.27  Score=47.52  Aligned_cols=72  Identities=19%  Similarity=0.431  Sum_probs=48.2

Q ss_pred             HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022126          110 AMQEKFTEKL---EQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRS  181 (302)
Q Consensus       110 ~L~~~l~~ki---~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rs  181 (302)
                      .++++|++-+   .++..+-..|.=++.-|+..++.+...+.+|++.|+||+|.+..+...++.|+.++..+|..
T Consensus        88 evEekyrkAMv~naQLDNek~~l~yqvd~Lkd~lee~eE~~~~~~re~~eK~~elEr~K~~~d~L~~e~~~Lre~  162 (302)
T PF09738_consen   88 EVEEKYRKAMVSNAQLDNEKSALMYQVDLLKDKLEELEETLAQLQREYREKIRELERQKRAHDSLREELDELREQ  162 (302)
T ss_pred             HHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455554432   12333333344445666777777777777888888999999999999999998888876553

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.

>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules

Probab=95.28  E-value=0.28  Score=45.01  Aligned_cols=76  Identities=18%  Similarity=0.344  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          101 VAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKR----CQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       101 ~~~lreK~e~L~~~l~~ki~e~~s~~~kl~~k----l~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +....++|..|..+..+++..+|..|+++..+    +..+++.+.-.+-+++.|.+.++.|+++...|+.+.|.|=.+++
T Consensus       127 l~~~eqry~aLK~hAeekL~~ANeei~~v~~~~~~e~~aLqa~lkk~e~~~~SLe~~LeQK~kEn~ELtkICDeLI~k~~  206 (207)
T PF05010_consen  127 LKKEEQRYQALKAHAEEKLEKANEEIAQVRSKHQAELLALQASLKKEEMKVQSLEESLEQKTKENEELTKICDELISKMG  206 (207)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34666788888888889999999999887654    45678888888889999999999999999999999999988754

The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].

>PRK11637 AmiB activator; Provisional

Probab=95.25  E-value=0.38  Score=48.00  Aligned_cols=59  Identities=8%  Similarity=0.116  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      ++.++..+++.+..++..++.+++.+++++.+++..+.+...++.++++-++.++..+.
T Consensus        69 ~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~  127 (428)
T PRK11637         69 QRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLA  127 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444444444444444444444444444444444444443

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=95.24  E-value=0.0071  Score=44.41  Aligned_cols=36  Identities=22%  Similarity=0.502  Sum_probs=28.7

Q ss_pred             CcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCC
Q 022126           13 RAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLM   50 (302)
Q Consensus        13 ~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~di   50 (302)
                      .-++..|||+.|..|..-.  +-.-||.|++++...++
T Consensus        19 ~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~~   54 (55)
T PF14447_consen   19 KGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDDP   54 (55)
T ss_pred             ccccccccceeeccccChh--hccCCCCCCCcccCCCC
Confidence            4678999999999996553  56789999999875543

>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.21  E-value=0.0071  Score=57.47  Aligned_cols=62  Identities=18%  Similarity=0.427  Sum_probs=43.4

Q ss_pred             ccccCcccccC---------CcEEecCCccccHHHHHhhh--cCCCCCCCCccccccCCCcccccCCChHHHHHHhcC
Q 022126            2 RCNACWRELEG---------RAISTTCGHLLCTEDANKIL--SNDAACPICDQVLSKSLMKPVDINPNDEWVNMAMAG   68 (302)
Q Consensus         2 ~CNiC~~~l~~---------~~vvT~CGHiFC~~Ci~~~~--~~~~~CPvC~~~l~~~div~~~LnPse~~Kt~vL~G   68 (302)
                      .|.+|.+.+..         +....+|+|+|-+.||..|.  .+..+||-|++...   +...-.||.|.  .-+++|
T Consensus       226 vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd---l~rmfsnpWek--ph~~yg  298 (328)
T KOG1734|consen  226 VCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD---LKRMFSNPWEK--PHVWYG  298 (328)
T ss_pred             hhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh---HhhhccCcccc--chhHHH
Confidence            48899987742         45678999999999999985  46889999999753   22223355543  334444

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

Probab=95.11  E-value=0.17  Score=46.72  Aligned_cols=61  Identities=16%  Similarity=0.293  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          116 TEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       116 ~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      .++........++++.++++.+.+++...+++.+|++..+++.+++..|-+-|.+|+.+++
T Consensus       150 ~~~~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~  210 (216)
T KOG1962|consen  150 EEENDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIE  210 (216)
T ss_pred             hhhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHh
Confidence            3344555666667777777777888888888888888888888888888888888888755

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.10  E-value=0.0095  Score=58.41  Aligned_cols=45  Identities=27%  Similarity=0.657  Sum_probs=35.2

Q ss_pred             ccccCcccccCCc-------EEecCCccccHHHHHhhh--cC-----CCCCCCCccccc
Q 022126            2 RCNACWRELEGRA-------ISTTCGHLLCTEDANKIL--SN-----DAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~~~-------vvT~CGHiFC~~Ci~~~~--~~-----~~~CPvC~~~l~   46 (302)
                      .|-||...+...+       ++-.|-|.||..||.+|-  ..     ...||.|+....
T Consensus       163 ~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  163 ECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            5889998875433       346799999999999996  33     578999998754

>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0

Probab=95.05  E-value=0.014  Score=50.14  Aligned_cols=47  Identities=21%  Similarity=0.544  Sum_probs=37.6

Q ss_pred             ccccCcccccCCcEEe---cCCccccHHHHHhhhcC---CCCCCCCccccccC
Q 022126            2 RCNACWRELEGRAIST---TCGHLLCTEDANKILSN---DAACPICDQVLSKS   48 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT---~CGHiFC~~Ci~~~~~~---~~~CPvC~~~l~~~   48 (302)
                      .||||.+.-.+.-++.   -||-..|-.|-...|+.   -..||+|++.+..+
T Consensus        82 eCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss  134 (140)
T PF05290_consen   82 ECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS  134 (140)
T ss_pred             eccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence            6999998765544444   49999999999999874   56899999998654

>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

Probab=94.99  E-value=0.02  Score=45.30  Aligned_cols=33  Identities=18%  Similarity=0.381  Sum_probs=29.5

Q ss_pred             cEEecCCccccHHHHHhhhcCCCCCCCCccccc
Q 022126           14 AISTTCGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus        14 ~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      .+.-.|.|.|=..||.+|+.....||.|++...
T Consensus        49 v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~   81 (88)
T COG5194          49 VVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWV   81 (88)
T ss_pred             EEEEecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence            456789999999999999999999999998764

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.86  E-value=0.63  Score=42.66  Aligned_cols=64  Identities=11%  Similarity=0.202  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          111 MQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       111 L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      +.+++.+...+.+..-..++.+++..+.+...|+.+|++|++.+.+-..+...|+...+.++..
T Consensus       105 l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~~  168 (206)
T PRK10884        105 LTDKLNNIDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLDDKQRT  168 (206)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333334445555556666666677777777666666666666666556666554

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=94.51  E-value=0.029  Score=40.16  Aligned_cols=44  Identities=30%  Similarity=0.756  Sum_probs=27.7

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      -|-.||-.-  +..|.-=.|-.|..|+...++.+..||+|+++|..
T Consensus         4 nCKsCWf~~--k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen    4 NCKSCWFAN--KGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             ---SS-S----SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             cChhhhhcC--CCeeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            477899664  35555557999999999999999999999998853

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. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

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

Probab=94.30  E-value=3.4  Score=37.20  Aligned_cols=35  Identities=23%  Similarity=0.459  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 022126          115 FTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQE  149 (302)
Q Consensus       115 l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~E  149 (302)
                      +...+.+++.++..|..++.+++...+.++++.+|
T Consensus       125 l~~~i~~L~~e~~~L~~~~~~l~~~~e~~ek~~~e  159 (189)
T PF10211_consen  125 LEEEIEELEEEKEELEKQVQELKNKCEQLEKREEE  159 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444443

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

>PF04949 Transcrip_act: Transcriptional activator; InterPro: IPR007033 Golgins are a family of coiled-coil proteins associated with the Golgi apparatus necessary for tethering events in membrane fusion and as structural supports for Golgi cisternae []

Probab=94.12  E-value=2  Score=37.70  Aligned_cols=63  Identities=24%  Similarity=0.333  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          117 EKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMK  179 (302)
Q Consensus       117 ~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~  179 (302)
                      +-+.-+.+.|+.+.+.+..+-.-+..-+++..|-.+.|.||++++.+|-+-...|..+.|.+|
T Consensus        84 kEv~~vRkkID~vNreLkpl~~~cqKKEkEykealea~nEknkeK~~Lv~~L~eLv~eSE~~r  146 (159)
T PF04949_consen   84 KEVEMVRKKIDSVNRELKPLGQSCQKKEKEYKEALEAFNEKNKEKAQLVTRLMELVSESERLR  146 (159)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444455555555555555555555777888889999999999999988888888877654

This entry represents proteins annotated as RAB6-interacting golgins.

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=93.96  E-value=0.019  Score=57.12  Aligned_cols=45  Identities=24%  Similarity=0.578  Sum_probs=36.0

Q ss_pred             CccccCcccccC---CcEEecCCccccHHHHHhhhcC--CCCCCCCcccc
Q 022126            1 MRCNACWRELEG---RAISTTCGHLLCTEDANKILSN--DAACPICDQVL   45 (302)
Q Consensus         1 l~CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~~~--~~~CPvC~~~l   45 (302)
                      +.|+.|.+.+.-   .--..+|+|||-..|+..++++  +++||.|++-.
T Consensus       366 L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crklr  415 (518)
T KOG1941|consen  366 LYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLR  415 (518)
T ss_pred             hhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence            469999988742   3346789999999999998764  88999999543

>PRK02224 chromosome segregation protein; Provisional

Probab=93.79  E-value=4.3  Score=43.83  Aligned_cols=17  Identities=29%  Similarity=0.571  Sum_probs=13.5

Q ss_pred             CCCCCCCCccccccCCC
Q 022126           34 NDAACPICDQVLSKSLM   50 (302)
Q Consensus        34 ~~~~CPvC~~~l~~~di   50 (302)
                      ....||+|++++...++
T Consensus       450 ~~~~Cp~C~r~~~~~~~  466 (880)
T PRK02224        450 EAGKCPECGQPVEGSPH  466 (880)
T ss_pred             hcccCCCCCCcCCCcch
Confidence            35789999999977654

>PRK10884 SH3 domain-containing protein; Provisional

Probab=93.49  E-value=1.7  Score=39.77  Aligned_cols=46  Identities=13%  Similarity=0.080  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          133 CQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      ..+|+.++++..+.+.||.+.+.+=..++.++++--+.|+.+.+..
T Consensus       120 ~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~  165 (206)
T PRK10884        120 TAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLDDK  165 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444455555555555555555555555555555555554433

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

Probab=93.49  E-value=5.5  Score=38.67  Aligned_cols=45  Identities=18%  Similarity=0.327  Sum_probs=25.2

Q ss_pred             HhcCCChHHHHHHHHHhhhhhhhhhHHHHHHH---HHHHHHHHHHHHHHH
Q 022126           65 AMAGVSPQILMKSAYRSVMFYLGQKELEMQYK---MNRIVAQCRQKCEAM  111 (302)
Q Consensus        65 vL~GlsP~~Ime~a~RAi~Fw~~Q~~qe~~yQ---~~~l~~~lreK~e~L  111 (302)
                      -|-|-+|-.+|=.|+ |+ |+.||...+..-.   .-.-++.+++|++.|
T Consensus        20 gLvGGp~Gl~ml~Ag-A~-Y~~yQ~~EQAr~~A~~fA~~ld~~~~kl~~M   67 (301)
T PF06120_consen   20 GLVGGPPGLVMLGAG-AW-YYFYQNAEQARQEAIEFADSLDELKEKLKEM   67 (301)
T ss_pred             HhhcchHHHHHHHHH-HH-HHHHHHHHHHHHHHHHHHHhhHHHHHHHHhc
Confidence            367889999986554 44 4456665542211   112345666665555

>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids []

Probab=93.42  E-value=1.7  Score=33.45  Aligned_cols=57  Identities=19%  Similarity=0.342  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 022126          108 CEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKL  164 (302)
Q Consensus       108 ~e~L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qL  164 (302)
                      .+.|++.|+++..+-.++|..++.....+.++...|+..+.+|......=+++...|
T Consensus        12 le~Lq~~y~~q~~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql~rL   68 (70)
T PF04899_consen   12 LEELQQSYEKQQQEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLSEQLERL   68 (70)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            357888999999999999999998888888888899999888877777666665554

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=93.20  E-value=1.1  Score=35.34  Aligned_cols=55  Identities=18%  Similarity=0.395  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          120 EQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       120 ~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      +++++.|+++-..+.-++-|++.|+.+|..|.+...+-......|..-..+||.+
T Consensus         7 eqLE~KIqqAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E   61 (79)
T PRK15422          7 EKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQ   61 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            3344444444445666777777777777777766554333333344444444433

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

Probab=93.18  E-value=0.81  Score=37.85  Aligned_cols=61  Identities=26%  Similarity=0.394  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHH
Q 022126          115 FTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSR---------QKRKLDEMYDQLRSEY  175 (302)
Q Consensus       115 l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsR---------q~~qLqelYdkLK~~~  175 (302)
                      +++.+.++..++..|+..+.++-.|...|+.+|+.|.+.+.+...         ...++.+.|+.|.+=|
T Consensus        13 le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~~~~~~~~~~~~~~~~~g~~NL~~LY   82 (107)
T PF06156_consen   13 LEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQEEEEKEEKKTKKKLGEGRDNLARLY   82 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccchHHHHHHHH
Confidence            445666677777888888889989999999999999988876533         2234445555555443

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

>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=93.03  E-value=7.7  Score=36.20  Aligned_cols=45  Identities=18%  Similarity=0.395  Sum_probs=27.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022126          137 EQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRS  181 (302)
Q Consensus       137 e~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rs  181 (302)
                      .++...|...+.++...-+..-....++++-|..||.+++.+|.+
T Consensus        59 ~~DIn~lE~iIkqa~~er~~~~~~i~r~~eey~~Lk~~in~~R~e  103 (230)
T PF10146_consen   59 NQDINTLENIIKQAESERNKRQEKIQRLYEEYKPLKDEINELRKE  103 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333445577778888999999988887

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.

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

Probab=92.73  E-value=1  Score=41.76  Aligned_cols=61  Identities=23%  Similarity=0.390  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022126          122 VHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSA  182 (302)
Q Consensus       122 ~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa  182 (302)
                      ++.+.+++..++..++.|++...++.+.++++..+=.+|...++.-||.|..++.+++...
T Consensus       149 ~~~~~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i  209 (216)
T KOG1962|consen  149 LEEENDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQI  209 (216)
T ss_pred             hhhhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHH
Confidence            4556677777777788888888888888888888888888999999999998888886653

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

Probab=92.71  E-value=2.1  Score=34.34  Aligned_cols=37  Identities=22%  Similarity=0.487  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 022126          131 KRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEM  167 (302)
Q Consensus       131 ~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqel  167 (302)
                      .++..++.++..+.+++++|+.++.-...+.++|-.+
T Consensus        49 k~v~~L~~e~~~l~~E~e~L~~~l~~e~~Ek~~Ll~l   85 (87)
T PF12709_consen   49 KKVDELENENKALKRENEQLKKKLDTEREEKQELLKL   85 (87)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3566677777777777777777776555555555444

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

>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B

Probab=92.66  E-value=0.099  Score=37.45  Aligned_cols=43  Identities=28%  Similarity=0.626  Sum_probs=23.0

Q ss_pred             cccCccccc--C-CcEEecCCccccHHHHHhhhc-CCCCCCCCcccc
Q 022126            3 CNACWRELE--G-RAISTTCGHLLCTEDANKILS-NDAACPICDQVL   45 (302)
Q Consensus         3 CNiC~~~l~--~-~~vvT~CGHiFC~~Ci~~~~~-~~~~CPvC~~~l   45 (302)
                      |++|-..+.  + ...--.||+-.|..|..+..+ ....||.|+++.
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            788888874  2 345567999999999999986 488999999864

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

Probab=92.62  E-value=0.87  Score=33.56  Aligned_cols=46  Identities=15%  Similarity=0.378  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          128 KMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRS  173 (302)
Q Consensus       128 kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~  173 (302)
                      .+.+++..++..+..++++|++|.+..++-.+-.++|-.||+-+=+
T Consensus         4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ll~lYE~Vs~   49 (55)
T PF05377_consen    4 ELENELPRIESSINTVKKENEEISESVEKIEENVKDLLSLYEVVSN   49 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            3444555556666777777777777777667777888888876644

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

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

Probab=92.58  E-value=2.8  Score=40.56  Aligned_cols=22  Identities=27%  Similarity=0.418  Sum_probs=9.5

Q ss_pred             HHHHHHHhhhhhhhhhHHHHHH
Q 022126           74 LMKSAYRSVMFYLGQKELEMQY   95 (302)
Q Consensus        74 Ime~a~RAi~Fw~~Q~~qe~~y   95 (302)
                      +|+.=.+.+.=++-...-.+.|
T Consensus       119 ~m~~q~~~vK~~aRl~aK~~WY  140 (325)
T PF08317_consen  119 LMDNQFQLVKTYARLEAKKMWY  140 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            4544444444444444444444

>KOG4001 consensus Axonemal dynein light chain [Cytoskeleton]

Probab=92.51  E-value=4  Score=37.84  Aligned_cols=92  Identities=16%  Similarity=0.233  Sum_probs=53.6

Q ss_pred             hhhhhhhhHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 022126           82 VMFYLGQKELE--MQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSR  159 (302)
Q Consensus        82 i~Fw~~Q~~qe--~~yQ~~~l~~~lreK~e~L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsR  159 (302)
                      +.|-+||...+  +.|-|.+.+..     +.-...++.++..++..-..|..++++|+..++.-++.+.|+.+.-+.|-.
T Consensus       160 Mt~aAYqtlyeSsvAfGmRKALqa-----e~ek~~~~~~~k~le~~k~~Le~~ia~~k~K~e~~e~r~~E~r~ieEkk~~  234 (259)
T KOG4001|consen  160 MTFAAYQTLYESSVAFGMRKALQA-----ENEKTRATTEWKVLEDKKKELELKIAQLKKKLETDEIRSEEEREIEEKKMK  234 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-----hhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            45678888776  33444332211     122334455666666666667777777877777777777777554443332


Q ss_pred             -HHHHHHHHHHHHHHHHHHH
Q 022126          160 -QKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       160 -q~~qLqelYdkLK~~~e~~  178 (302)
                       +..-|.+--.+||++++.+
T Consensus       235 eei~fLk~tN~qLKaQLegI  254 (259)
T KOG4001|consen  235 EEIEFLKETNRQLKAQLEGI  254 (259)
T ss_pred             HHHHHHHHHHHHHHHHHhhc
Confidence             3455555566777776543

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

Probab=92.38  E-value=2.7  Score=40.71  Aligned_cols=64  Identities=22%  Similarity=0.459  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          113 EKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       113 ~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +.+.+.+.+++.+...+...+.+++.+.+.+.++-.++-+.|.+...++.++++-.+.|+.+++
T Consensus        60 ~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e~~sl~~q~~  123 (314)
T PF04111_consen   60 EELLQELEELEKEREELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEERDSLKNQYE  123 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444445555555555555555555555555555545555555555444444444444444443

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.

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=92.37  E-value=0.037  Score=61.77  Aligned_cols=46  Identities=26%  Similarity=0.598  Sum_probs=40.7

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      +.|.+|.+.+.+.-.++.|||.+|..|..-|......||+|+....
T Consensus      1154 ~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi~~ 1199 (1394)
T KOG0298|consen 1154 FVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICKSIKG 1199 (1394)
T ss_pred             cchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchhhhhh
Confidence            3699999999867779999999999999999999999999996553

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

Probab=92.36  E-value=4.1  Score=31.40  Aligned_cols=30  Identities=13%  Similarity=0.391  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 022126          122 VHTAYQKMAKRCQMMEQEIESLSKDKQELQ  151 (302)
Q Consensus       122 ~~s~~~kl~~kl~~me~E~e~LrKkn~ELq  151 (302)
                      +..++..|+.+...+..+.+.|+.+|+.|+
T Consensus        23 Lq~e~eeLke~n~~L~~e~~~L~~en~~L~   52 (72)
T PF06005_consen   23 LQMENEELKEKNNELKEENEELKEENEQLK   52 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            333444444444555555555555555555

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

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

Probab=92.02  E-value=3.3  Score=34.94  Aligned_cols=49  Identities=31%  Similarity=0.432  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          127 QKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEY  175 (302)
Q Consensus       127 ~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~  175 (302)
                      .....++..++.+++.|+.+.+-+-+.|-||+-+...|+.-...||.=|
T Consensus        64 ~~~~~~~~~L~~el~~l~~ry~t~LellGEK~E~veEL~~Dv~DlK~my  112 (120)
T PF12325_consen   64 RALKKEVEELEQELEELQQRYQTLLELLGEKSEEVEELRADVQDLKEMY  112 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHH
Confidence            3344556777888888888888888888899999888887777777554

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

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

Probab=92.00  E-value=6.2  Score=39.15  Aligned_cols=44  Identities=32%  Similarity=0.480  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHH
Q 022126          133 CQMMEQEIESLSKDKQELQEKF-------SEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky-------~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +..+-.+....+.+..+++++|       .++++++.++.+-.+++|.+++
T Consensus       268 le~l~~eYr~~~~~ls~~~~~y~~~s~~V~~~t~~L~~IseeLe~vK~eme  318 (359)
T PF10498_consen  268 LEPLIQEYRSAQDELSEVQEKYKQASEGVSERTRELAEISEELEQVKQEME  318 (359)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444       4455566666666666666543

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

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=91.91  E-value=1.9  Score=38.28  Aligned_cols=55  Identities=20%  Similarity=0.375  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022126          129 MAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSAI  183 (302)
Q Consensus       129 l~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa~  183 (302)
                      +......++.++..|+.+|.+|..++++...++..+++-|..|-.=++.+|.-+.
T Consensus       102 ~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~Im~RARkl~~  156 (161)
T TIGR02894       102 LQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDIMDRARKLAV  156 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3444556777777888888888888888888888889999998888887776543

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

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

Probab=91.91  E-value=1.3  Score=48.06  Aligned_cols=50  Identities=16%  Similarity=0.290  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022126          133 CQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSA  182 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa  182 (302)
                      ++.+.+....|+-+++||.++|.++.-++.||.+-|+.||.+++.++.++
T Consensus       673 ~e~lkQ~~~~l~~e~eeL~~~vq~~~s~hsql~~q~~~Lk~qLg~~~~~~  722 (970)
T KOG0946|consen  673 IENLKQMEKELQVENEELEEEVQDFISEHSQLKDQLDLLKNQLGIISSKQ  722 (970)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccch
Confidence            34444555666777888999999999999999999999999988554443

>TIGR01069 mutS2 MutS2 family protein

Probab=91.87  E-value=6.2  Score=42.82  Aligned_cols=17  Identities=12%  Similarity=0.052  Sum_probs=11.3

Q ss_pred             hHHHHHHhcCCChHHHH
Q 022126           59 DEWVNMAMAGVSPQILM   75 (302)
Q Consensus        59 e~~Kt~vL~GlsP~~Im   75 (302)
                      .-....-..|+++++|-
T Consensus       484 ~a~~iA~~~Glp~~ii~  500 (771)
T TIGR01069       484 YAFEIAQRYGIPHFIIE  500 (771)
T ss_pred             HHHHHHHHhCcCHHHHH
Confidence            33444567899888776

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

>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins

Probab=91.65  E-value=0.19  Score=35.67  Aligned_cols=41  Identities=22%  Similarity=0.630  Sum_probs=32.5

Q ss_pred             ccccCccccc-CCcEEecCC-----ccccHHHHHhhhcC--CCCCCCCc
Q 022126            2 RCNACWRELE-GRAISTTCG-----HLLCTEDANKILSN--DAACPICD   42 (302)
Q Consensus         2 ~CNiC~~~l~-~~~vvT~CG-----HiFC~~Ci~~~~~~--~~~CPvC~   42 (302)
                      .|-||+.... +.++++.|.     |.|=..|+.+|+..  ...||+|+
T Consensus         1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4789987322 578999995     88999999999853  56899996

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.59  E-value=1.8  Score=41.28  Aligned_cols=38  Identities=13%  Similarity=0.387  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFS  155 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~  155 (302)
                      .|+.+..+++.+..++++.+.+.+.++.++.+|+.+..
T Consensus        53 ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~   90 (265)
T COG3883          53 EIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIA   90 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333344444444444444444433333

>KOG4367 consensus Predicted Zn-finger protein [Function unknown]

Probab=91.52  E-value=0.095  Score=53.01  Aligned_cols=31  Identities=32%  Similarity=0.635  Sum_probs=26.9

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhh
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKIL   32 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~   32 (302)
                      ++|++|...+ .+|+|.+|||..|..|+....
T Consensus         5 lkc~vc~~f~-~epiil~c~h~lc~~ca~~~~   35 (699)
T KOG4367|consen    5 LKCPVCGSFY-REPIILPCSHNLCQACARNIL   35 (699)
T ss_pred             ccCceehhhc-cCceEeecccHHHHHHHHhhc
Confidence            6899999776 479999999999999997653

>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=91.41  E-value=3.8  Score=42.75  Aligned_cols=51  Identities=18%  Similarity=0.379  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          125 AYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEY  175 (302)
Q Consensus       125 ~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~  175 (302)
                      .+.+|+.+..++....+.+..++.+|...+.+...++.+|++-+..|..+.
T Consensus       186 e~e~L~~~~kel~~~~e~l~~E~~~L~~q~~e~~~ri~~LEedi~~l~qk~  236 (546)
T PF07888_consen  186 EMEQLKQQQKELTESSEELKEERESLKEQLAEARQRIRELEEDIKTLTQKE  236 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555566666666777777777777776666777776666665443

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 [].

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

Probab=91.38  E-value=3.2  Score=35.86  Aligned_cols=41  Identities=27%  Similarity=0.414  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKS  158 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKs  158 (302)
                      ...+++.+|..|.+|+..++.+++.+..+..+++.++.+..
T Consensus        29 ~~~~~E~EI~sL~~K~~~lE~eld~~~~~l~~~k~~lee~~   69 (143)
T PF12718_consen   29 ENEQKEQEITSLQKKNQQLEEELDKLEEQLKEAKEKLEESE   69 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence            44444555555555555555555555555555555555444

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 [].

>PRK10780 periplasmic chaperone; Provisional

Probab=91.34  E-value=5.8  Score=34.57  Aligned_cols=50  Identities=6%  Similarity=0.058  Sum_probs=22.2

Q ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126           82 VMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAK  131 (302)
Q Consensus        82 i~Fw~~Q~~qe~~yQ~~~l~~~lreK~e~L~~~l~~ki~e~~s~~~kl~~  131 (302)
                      ++|-..|.-+.-.=+...+.+.+..+.+..+..++.+..++...+++++.
T Consensus        26 Ig~Vd~q~il~~~p~~k~~~~~le~~~~~~q~el~~~~~elq~~~~~~q~   75 (165)
T PRK10780         26 IAIVNMGSIFQQVPQRTGVSKQLENEFKGRASELQRMETDLQAKMQKLQR   75 (165)
T ss_pred             eEEeeHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45555555433221222344444444444444444444455444444443

>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=91.33  E-value=0.086  Score=55.41  Aligned_cols=40  Identities=25%  Similarity=0.682  Sum_probs=31.4

Q ss_pred             CccccCccccc---CCcEEecCCccccHHHHHhhhcCCCCCCCCcc
Q 022126            1 MRCNACWRELE---GRAISTTCGHLLCTEDANKILSNDAACPICDQ   43 (302)
Q Consensus         1 l~CNiC~~~l~---~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~   43 (302)
                      +.|.||...+.   -.||...|||+.|..|+...  ...+|| |+.
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~   54 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR   54 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence            46999966653   36999999999999999987  356788 554

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=91.29  E-value=7.9  Score=40.97  Aligned_cols=34  Identities=24%  Similarity=0.461  Sum_probs=19.0

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          139 EIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLR  172 (302)
Q Consensus       139 E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK  172 (302)
                      |.+.+.+++..|..+|+|+.+...+|..-.+.|+
T Consensus       475 ei~~~~~~I~~L~~~L~e~~~~ve~L~~~l~~l~  508 (652)
T COG2433         475 EIRARDRRIERLEKELEEKKKRVEELERKLAELR  508 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444555556666666666665555555555554

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

Probab=91.09  E-value=6.2  Score=37.25  Aligned_cols=66  Identities=23%  Similarity=0.523  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          111 MQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       111 L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +...|...+.++...++.+......++.+.+.++.+..+++.+|++.......++.-...||..++
T Consensus        48 ~~~~ye~el~~lr~~id~~~~eka~l~~e~~~l~~e~~~~r~k~e~e~~~~~~le~el~~lrk~ld  113 (312)
T PF00038_consen   48 IKEMYEEELRELRRQIDDLSKEKARLELEIDNLKEELEDLRRKYEEELAERKDLEEELESLRKDLD  113 (312)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccchhhHHHHhHHhhhhHHHHhhHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Confidence            344455566666666666666566666666666777777766666666666666665555555544

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 ....

>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs

Probab=91.08  E-value=5.7  Score=42.80  Aligned_cols=16  Identities=19%  Similarity=0.177  Sum_probs=9.8

Q ss_pred             ChHHHHHHHHHhhhhh
Q 022126           70 SPQILMKSAYRSVMFY   85 (302)
Q Consensus        70 sP~~Ime~a~RAi~Fw   85 (302)
                      ++.+.++...+|+...
T Consensus       533 ~~~E~l~lL~~a~~vl  548 (717)
T PF10168_consen  533 SPQECLELLSQATKVL  548 (717)
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            4556677777776543

It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].

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

Probab=91.04  E-value=8.8  Score=42.94  Aligned_cols=84  Identities=24%  Similarity=0.372  Sum_probs=57.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHhh-c-CCC
Q 022126          113 EKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM----KRSA-I-QPS  186 (302)
Q Consensus       113 ~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~----~rsa-~-~~a  186 (302)
                      +.++..+.+++..+..|+..+..++.....|+.+.+++.+++.+...++-.++.....|+++.+..    +... . ...
T Consensus       390 ~~~~~~~~e~e~k~~~L~~evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~l~k~i~~~~~~l~~lk~~k~dk  469 (1074)
T KOG0250|consen  390 NELGSELEERENKLEQLKKEVEKLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQLRKKIENISEELKDLKKTKTDK  469 (1074)
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccch
Confidence            334455566666677777777778888888888888888888888888888888888888776633    2222 2 234


Q ss_pred             CCCCCCCCCC
Q 022126          187 NSFYPRNDPD  196 (302)
Q Consensus       187 ~~~~~~~~~~  196 (302)
                      .++|+.+-|.
T Consensus       470 vs~FG~~m~~  479 (1074)
T KOG0250|consen  470 VSAFGPNMPQ  479 (1074)
T ss_pred             hhhcchhhHH
Confidence            4567755443

>smart00787 Spc7 Spc7 kinetochore protein

Probab=90.96  E-value=15  Score=35.65  Aligned_cols=29  Identities=21%  Similarity=0.353  Sum_probs=11.6

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          145 KDKQELQEKFSEKSRQKRKLDEMYDQLRS  173 (302)
Q Consensus       145 Kkn~ELq~ky~EKsRq~~qLqelYdkLK~  173 (302)
                      .+.++|..+.++...++.++++..+.+.+
T Consensus       232 ~~l~~l~~~I~~~~~~k~e~~~~I~~ae~  260 (312)
T smart00787      232 EELQELESKIEDLTNKKSELNTEIAEAEK  260 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333334444444444444444333

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

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

Probab=90.89  E-value=1  Score=43.91  Aligned_cols=62  Identities=19%  Similarity=0.376  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          117 EKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       117 ~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      +++.+++..+...+.++...+.++..+..++.+|+..|++..++..+|+.-++....+++.+
T Consensus       221 ~~l~~a~~~l~~~~~~L~~~~~~l~~l~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~kl~rA  282 (344)
T PF12777_consen  221 QKLEEAEAELEEAEEQLAEKQAELAELEEKLAALQKEYEEAQKEKQELEEEIEETERKLERA  282 (344)
T ss_dssp             HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccH
Confidence            44455555555556666666667777777777777777777777777777777666665544

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=90.89  E-value=0.1  Score=51.33  Aligned_cols=56  Identities=23%  Similarity=0.571  Sum_probs=44.4

Q ss_pred             ccccCccccc---CCcEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCCcccccCC
Q 022126            2 RCNACWRELE---GRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLMKPVDINP   57 (302)
Q Consensus         2 ~CNiC~~~l~---~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~div~~~LnP   57 (302)
                      .|+.|..++.   ..++-..||--.|.-|....-.+ ...||+|++...+..+-.+.|.|
T Consensus        16 ~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~~~s~   75 (480)
T COG5175          16 YCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVTLSP   75 (480)
T ss_pred             cCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEEecCH
Confidence            4999999874   35778899999999998877554 77999999999887775555544

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

Probab=90.75  E-value=1.5  Score=39.30  Aligned_cols=55  Identities=18%  Similarity=0.371  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          122 VHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       122 ~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +...+.....++..++.+...|+.++.+|.+.++||.+-+.-|+.-|..|.-++.
T Consensus       107 l~~~~~~~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~  161 (194)
T PF08614_consen  107 LEKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQLN  161 (194)
T ss_dssp             -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333444455555555555555555555555555555555555555444443

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.

>smart00787 Spc7 Spc7 kinetochore protein

Probab=90.75  E-value=6.6  Score=38.18  Aligned_cols=38  Identities=29%  Similarity=0.309  Sum_probs=14.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          137 EQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       137 e~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      ..+++..+++..|+++.+.+..-.+....+.-..+..+
T Consensus       217 ~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~  254 (312)
T smart00787      217 LQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTE  254 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333333333333333

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

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=90.64  E-value=8.1  Score=41.99  Aligned_cols=26  Identities=8%  Similarity=0.083  Sum_probs=15.5

Q ss_pred             ChHHHHHHhcCCChHHHHHHHHHhhhhhhh
Q 022126           58 NDEWVNMAMAGVSPQILMKSAYRSVMFYLG   87 (302)
Q Consensus        58 se~~Kt~vL~GlsP~~Ime~a~RAi~Fw~~   87 (302)
                      |.-....-..|+++++|-    +|-.++..
T Consensus       488 S~a~~iA~~~Glp~~ii~----~A~~~~~~  513 (782)
T PRK00409        488 SNAFEIAKRLGLPENIIE----EAKKLIGE  513 (782)
T ss_pred             cHHHHHHHHhCcCHHHHH----HHHHHHhh
Confidence            333444567899888876    44444443

>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional

Probab=90.63  E-value=8.7  Score=42.87  Aligned_cols=45  Identities=24%  Similarity=0.491  Sum_probs=30.9

Q ss_pred             ccccCcccccC-CcEEecCC---ccccHHHHHhhhcC---CCCCCCCccccc
Q 022126            2 RCNACWRELEG-RAISTTCG---HLLCTEDANKILSN---DAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~-~~vvT~CG---HiFC~~Ci~~~~~~---~~~CPvC~~~l~   46 (302)
                      +|++|..++.+ ..++.--+   .--|..|..-....   -..||.|+-.+.
T Consensus       798 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  849 (1006)
T PRK12775        798 TCPKCHRPLEGDEEYVCCATSELQWRCDDCGKVSEGFAFPYGMCPACGGKLQ  849 (1006)
T ss_pred             cCcccCCCCCCCceeEEecCcceeeehhhhccccccccCCcCcCcccccchh
Confidence            69999999975 34433222   33499998776432   357999999864

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.58  E-value=3.6  Score=31.93  Aligned_cols=18  Identities=28%  Similarity=0.545  Sum_probs=7.6

Q ss_pred             HHHHHHHHHHHHhHHHHH
Q 022126          134 QMMEQEIESLSKDKQELQ  151 (302)
Q Consensus       134 ~~me~E~e~LrKkn~ELq  151 (302)
                      +-++-|.+.|+.||+.|+
T Consensus        21 ~LLQmEieELKEknn~l~   38 (79)
T COG3074          21 TLLQMEIEELKEKNNSLS   38 (79)
T ss_pred             HHHHHHHHHHHHHhhHhH
Confidence            334444444444444433

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

Probab=90.53  E-value=13  Score=33.52  Aligned_cols=52  Identities=27%  Similarity=0.421  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHH
Q 022126          128 KMAKRCQMMEQEIESLSKDKQELQEKFSEKS--------RQKRKLDEMYDQLRSEYESMK  179 (302)
Q Consensus       128 kl~~kl~~me~E~e~LrKkn~ELq~ky~EKs--------Rq~~qLqelYdkLK~~~e~~~  179 (302)
                      .+..++..++.+.+.|+++..+|..+++.-.        -+..+.++-++.||+...+++
T Consensus       124 ~l~~~i~~L~~e~~~L~~~~~~l~~~~e~~ek~~~e~~~~~~k~~~~ei~~lk~~~~ql~  183 (189)
T PF10211_consen  124 ELEEEIEELEEEKEELEKQVQELKNKCEQLEKREEELRQEEEKKHQEEIDFLKKQNQQLK  183 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444445555555555555555554443322        233445555666666655543

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

>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=90.39  E-value=0.17  Score=49.95  Aligned_cols=44  Identities=27%  Similarity=0.667  Sum_probs=36.4

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhh--hcCCCCCCCCcccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKI--LSNDAACPICDQVL   45 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~--~~~~~~CPvC~~~l   45 (302)
                      +.|-||-..++ ...+++|+|-.|..|+.+.  +-....||.|++.-
T Consensus        62 ~~C~ICA~~~T-Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          62 MNCQICAGSTT-YSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             ceeEEecCCce-EEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            46889998886 4669999999999999876  34688999999864

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

Probab=90.11  E-value=4.2  Score=35.78  Aligned_cols=44  Identities=30%  Similarity=0.410  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          133 CQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +..+..+...++++..++++...+...++..+++.|+.|.....
T Consensus       139 ~~~~~~e~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  182 (191)
T PF04156_consen  139 IKELEKEIRELQKELQDSREEVQELRSQLERLQENLQQLEEKIQ  182 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444434444445555555555666666666555543

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 [].

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

Probab=90.00  E-value=11  Score=32.08  Aligned_cols=64  Identities=19%  Similarity=0.406  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          113 EKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       113 ~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      ..++..+..+...+..++.++...+....++++++..+..+.+.-..+.+++.......+.+++
T Consensus        69 ~~l~~~~~rL~~~~~~~ere~~~~~~~~~~l~~~~~~~~~~~k~~kee~~klk~~~~~~~tq~~  132 (151)
T PF11559_consen   69 ERLQNDVERLKEQLEELERELASAEEKERQLQKQLKSLEAKLKQEKEELQKLKNQLQQRKTQYE  132 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555566666666666666666777777777777776666677777777777666665

pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.

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

Probab=89.91  E-value=11  Score=32.19  Aligned_cols=6  Identities=17%  Similarity=0.578  Sum_probs=2.2

Q ss_pred             HHHHHH
Q 022126          168 YDQLRS  173 (302)
Q Consensus       168 YdkLK~  173 (302)
                      |++||.
T Consensus       142 ~~kLk~  147 (151)
T PF11559_consen  142 IEKLKE  147 (151)
T ss_pred             HHHHHH
Confidence            333333

pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=89.85  E-value=3.3  Score=43.64  Aligned_cols=61  Identities=20%  Similarity=0.410  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Q 022126          115 FTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEK---SRQKRKLDEMYDQLRSEY  175 (302)
Q Consensus       115 l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EK---sRq~~qLqelYdkLK~~~  175 (302)
                      ++++++.+..+++.|+..+.+|+.+++.|+.+..++.+..+++   .|+++.+++-.+.|+.++
T Consensus       427 ~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r~~~~~~~~~rei~~~~~~I~~L~~~L  490 (652)
T COG2433         427 LEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKEL  490 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence            3344444445555555555555555555555555555555543   345555555555555444

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

Probab=89.85  E-value=3.2  Score=39.01  Aligned_cols=27  Identities=26%  Similarity=0.425  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          150 LQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       150 Lq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +++.++.-..++.+|++++++|--++.
T Consensus       168 ~~erlk~le~E~s~LeE~~~~l~~ev~  194 (290)
T COG4026         168 VQERLKRLEVENSRLEEMLKKLPGEVY  194 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhchhHHH
Confidence            333333333445555555554443333

>TIGR02680 conserved hypothetical protein TIGR02680

Probab=89.81  E-value=16  Score=42.23  Aligned_cols=29  Identities=21%  Similarity=0.051  Sum_probs=15.4

Q ss_pred             HHhcCCChHHHHHHHHHhhhhhhhhhHHH
Q 022126           64 MAMAGVSPQILMKSAYRSVMFYLGQKELE   92 (302)
Q Consensus        64 ~vL~GlsP~~Ime~a~RAi~Fw~~Q~~qe   92 (302)
                      .-|..+++..|-+++.....+-..+..++
T Consensus       212 ~~l~~l~~~~i~~l~e~~~~~~~~~~~le  240 (1353)
T TIGR02680       212 EALPPLDDDELTDVADALEQLDEYRDELE  240 (1353)
T ss_pred             HhCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555666666555555444544554444

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length.

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=89.68  E-value=2.8  Score=34.92  Aligned_cols=41  Identities=17%  Similarity=0.282  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 022126          116 TEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSE  156 (302)
Q Consensus       116 ~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~E  156 (302)
                      ++.+.++..++..|+..+.++-.|...|+-+|+-|.+.+.+
T Consensus        14 e~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~   54 (110)
T PRK13169         14 EQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEE   54 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555566666777777778878888888888888887775

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

Probab=89.64  E-value=17  Score=35.19  Aligned_cols=30  Identities=30%  Similarity=0.373  Sum_probs=11.8

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          142 SLSKDKQELQEKFSEKSRQKRKLDEMYDQL  171 (302)
Q Consensus       142 ~LrKkn~ELq~ky~EKsRq~~qLqelYdkL  171 (302)
                      .++.+.++|..+.++.+.++.+++.-+..+
T Consensus       234 el~~el~~l~~~i~~~~~~k~~l~~eI~e~  263 (325)
T PF08317_consen  234 ELQEELEELEEKIEELEEQKQELLAEIAEA  263 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333444444444443333

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.57  E-value=5.7  Score=37.91  Aligned_cols=63  Identities=8%  Similarity=0.222  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhc
Q 022126          121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE-SMKRSAI  183 (302)
Q Consensus       121 e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e-~~~rsa~  183 (302)
                      ++..+++.|..++.++..+.+.+++++.+++...++-..++..+.+-+.....-++ .+|..+.
T Consensus        49 ~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~~r~~~l~~raRAmq~  112 (265)
T COG3883          49 NIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVERQELLKKRARAMQV  112 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444444444444444444433333222222 2555555

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=89.56  E-value=7.8  Score=29.61  Aligned_cols=55  Identities=18%  Similarity=0.368  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          123 HTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYES  177 (302)
Q Consensus       123 ~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~  177 (302)
                      ...++.+..++...+.++..|+++.......+.++.....+|..-.+.|+.+++.
T Consensus        11 r~rLd~~~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~   65 (69)
T PF14197_consen   11 RNRLDSLTRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEE   65 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444555555666666666666666666666666666666666666666543

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

Probab=89.48  E-value=0.99  Score=31.78  Aligned_cols=32  Identities=28%  Similarity=0.492  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 022126          124 TAYQKMAKRCQMMEQEIESLSKDKQELQEKFS  155 (302)
Q Consensus       124 s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~  155 (302)
                      +.|+.|+.....+..|.+.|+.++.+|..++.
T Consensus        12 ~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~   43 (45)
T PF02183_consen   12 ASYDSLKAEYDSLKKENEKLRAEVQELKEKLQ   43 (45)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            34444444445555555666666655555543

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

>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A

Probab=89.44  E-value=0.13  Score=39.08  Aligned_cols=46  Identities=17%  Similarity=0.518  Sum_probs=22.3

Q ss_pred             CccccCccccc-C----CcEE--ecCCccccHHHHHhhhcC---C--------CCCCCCccccc
Q 022126            1 MRCNACWRELE-G----RAIS--TTCGHLLCTEDANKILSN---D--------AACPICDQVLS   46 (302)
Q Consensus         1 l~CNiC~~~l~-~----~~vv--T~CGHiFC~~Ci~~~~~~---~--------~~CPvC~~~l~   46 (302)
                      +.|.||+..+. +    ..+=  ..|+++|=..|+.+||..   .        ..||.|+++++
T Consensus         3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            46999998754 2    1222  268888888899999751   1        25999999875

>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp

Probab=89.37  E-value=6.6  Score=37.86  Aligned_cols=13  Identities=23%  Similarity=0.468  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHHHH
Q 022126          156 EKSRQKRKLDEMY  168 (302)
Q Consensus       156 EKsRq~~qLqelY  168 (302)
                      |-+-|..||+.|.
T Consensus       153 DINiQN~KLEsLL  165 (305)
T PF15290_consen  153 DINIQNKKLESLL  165 (305)
T ss_pred             hhhhhHhHHHHHH
Confidence            3334444444443

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

Probab=89.35  E-value=15  Score=32.50  Aligned_cols=16  Identities=25%  Similarity=0.356  Sum_probs=9.2

Q ss_pred             hcCCChHH---HHHHHHHh
Q 022126           66 MAGVSPQI---LMKSAYRS   81 (302)
Q Consensus        66 L~GlsP~~---Ime~a~RA   81 (302)
                      -+|++++.   |+++...+
T Consensus        13 ~~Gft~~QAe~i~~~l~~~   31 (177)
T PF07798_consen   13 AAGFTEEQAEAIMKALREV   31 (177)
T ss_pred             HCCCCHHHHHHHHHHHHHH
Confidence            46888873   55444444

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

Probab=89.33  E-value=4.3  Score=36.08  Aligned_cols=8  Identities=13%  Similarity=0.347  Sum_probs=3.1

Q ss_pred             HHHHHHHH
Q 022126          167 MYDQLRSE  174 (302)
Q Consensus       167 lYdkLK~~  174 (302)
                      -++.||.|
T Consensus       176 ~~~~LkkQ  183 (192)
T PF05529_consen  176 EIEALKKQ  183 (192)
T ss_pred             HHHHHHHH
Confidence            33333333

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

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

Probab=89.28  E-value=13  Score=31.75  Aligned_cols=58  Identities=9%  Similarity=0.244  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       121 e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      .+.+.|+.+-.|++++..-.+..+.+..|+++....-..+...++.+...|..++..+
T Consensus        65 hLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv~~i~~dv~~v~~~V~~Le~ki~~i  122 (126)
T PF07889_consen   65 HLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDVSQIGDDVDSVQQMVEGLEGKIDEI  122 (126)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344455555566666666677777888888888877778888888888887776654

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

>PHA03096 p28-like protein; Provisional

Probab=89.17  E-value=0.21  Score=47.88  Aligned_cols=42  Identities=12%  Similarity=0.196  Sum_probs=30.0

Q ss_pred             ccccCcccccC-------CcEEecCCccccHHHHHhhhcC---CCCCCCCcc
Q 022126            2 RCNACWRELEG-------RAISTTCGHLLCTEDANKILSN---DAACPICDQ   43 (302)
Q Consensus         2 ~CNiC~~~l~~-------~~vvT~CGHiFC~~Ci~~~~~~---~~~CPvC~~   43 (302)
                      .|.+|.+....       .-.+..|-|.||..|+..|...   ...||.|+.
T Consensus       180 ~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        180 ICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            48899886542       2457789999999999988642   445555555

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

Probab=88.95  E-value=8.5  Score=37.30  Aligned_cols=69  Identities=13%  Similarity=0.345  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022126          115 FTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSAI  183 (302)
Q Consensus       115 l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa~  183 (302)
                      +++...++..++..++.+...++.+.+..-+...+++..+.+...+...+..-|+.+..+++.+++..+
T Consensus        69 LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e~~sl~~q~~~~~~~L~~L~ktNv  137 (314)
T PF04111_consen   69 LEKEREELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEERDSLKNQYEYASNQLDRLRKTNV  137 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHT--T
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence            344556666777777777778877888888888999988988889999999999999999888888754

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.

>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []

Probab=88.82  E-value=16  Score=35.21  Aligned_cols=72  Identities=21%  Similarity=0.287  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHhhcCCCC--
Q 022126          124 TAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQK--------------RKLDEMYDQLRSEYESMKRSAIQPSN--  187 (302)
Q Consensus       124 s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~--------------~qLqelYdkLK~~~e~~~rsa~~~a~--  187 (302)
                      +.+..|+.....+-..+++|.+..+-|...+.-|.-+.              .+|+.-.-.+|.++|..+.++....+  
T Consensus        60 ~e~s~LkREnq~l~e~c~~lek~rqKlshdlq~Ke~qv~~lEgQl~s~Kkqie~Leqelkr~KsELErsQ~~~~~~~~sl  139 (307)
T PF10481_consen   60 NEYSALKRENQSLMESCENLEKTRQKLSHDLQVKESQVNFLEGQLNSCKKQIEKLEQELKRCKSELERSQQAASSGDVSL  139 (307)
T ss_pred             hhhhhhhhhhhhHHHHHHHHHHHHHHhhHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCccc
Confidence            33444444444444455555555555554444444333              33333444455665554444443332  


Q ss_pred             CCCCCCCC
Q 022126          188 SFYPRNDP  195 (302)
Q Consensus       188 ~~~~~~~~  195 (302)
                      +++..+.-
T Consensus       140 ~~~stpqk  147 (307)
T PF10481_consen  140 NPCSTPQK  147 (307)
T ss_pred             cccCCchh
Confidence            24554443

Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].

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

Probab=88.80  E-value=5.1  Score=29.67  Aligned_cols=49  Identities=20%  Similarity=0.443  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 022126          117 EKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMY  168 (302)
Q Consensus       117 ~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelY  168 (302)
                      .|+.++.+.++.|..|+..|..+...++-+   ++...+|-.|-...|.+.-
T Consensus         3 akid~Ls~dVq~L~~kvdqLs~dv~~lr~~---v~~ak~EAaRAN~RlDN~a   51 (56)
T PF04728_consen    3 AKIDQLSSDVQTLNSKVDQLSSDVNALRAD---VQAAKEEAARANQRLDNIA   51 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHhhH
Confidence            467778888888888888888888888875   4566778888888887653

The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.

>PHA02562 46 endonuclease subunit; Provisional

Probab=88.77  E-value=25  Score=35.70  Aligned_cols=51  Identities=22%  Similarity=0.393  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          126 YQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       126 ~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      ++.+..+...++.+++.++.+..+|.....+....+.+++..|.+++.+++
T Consensus       222 ~~~l~~~~~~l~~~l~~l~~~i~~l~~~i~~~~~~L~~l~~~~~~~~~~l~  272 (562)
T PHA02562        222 YDELVEEAKTIKAEIEELTDELLNLVMDIEDPSAALNKLNTAAAKIKSKIE  272 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHH
Confidence            333333333334444444444433333322333333444444444444433

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

Probab=88.69  E-value=12  Score=41.19  Aligned_cols=40  Identities=23%  Similarity=0.459  Sum_probs=20.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH
Q 022126          137 EQEIESLSKDKQELQEKFSEKSR-------QKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       137 e~E~e~LrKkn~ELq~ky~EKsR-------q~~qLqelYdkLK~~~e  176 (302)
                      +..++.+.++|.+|.+.+++-.|       |+....++|++||+++.
T Consensus       458 ~~s~~~~~~~~~~L~d~le~~~~~~~~~~~K~e~~~~~le~l~~El~  504 (980)
T KOG0980|consen  458 EQSIDDVEEENTNLNDQLEELQRAAGRAETKTESQAKALESLRQELA  504 (980)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            33444455555555555555444       34444455556655543

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

Probab=88.63  E-value=15  Score=41.30  Aligned_cols=47  Identities=19%  Similarity=0.402  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          132 RCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       132 kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      ++..+.+.++.++++..++..+|++++...++++.-++.|+++++.+
T Consensus       338 Ei~~~r~~~~~~~re~~~~~~~~~~~~n~i~~~k~~~d~l~k~I~~~  384 (1074)
T KOG0250|consen  338 EIEEARKDLDDLRREVNDLKEEIREIENSIRKLKKEVDRLEKQIADL  384 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45566777788888888999999998888888888888777776544

>KOG1850 consensus Myosin-like coiled-coil protein [Cytoskeleton]

Probab=88.51  E-value=12  Score=36.78  Aligned_cols=94  Identities=14%  Similarity=0.262  Sum_probs=48.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHh--hcCC--CCCCCCCCCCCCccccc-CCCCCccccccccc
Q 022126          146 DKQELQEKFSEKSRQKRKLDEMYDQLRSEYE----SMKRS--AIQP--SNSFYPRNDPDLFSANM-MDNRDPIRKDWSVY  216 (302)
Q Consensus       146 kn~ELq~ky~EKsRq~~qLqelYdkLK~~~e----~~~rs--a~~~--a~~~~~~~~~~~~~~~~-~~~~~~~r~~~~~~  216 (302)
                      ++.+--+.|+---.++++|+.||..|+-+-.    .+..-  .++.  |.--+..  |.+. |.| -|+..    .+.+-
T Consensus       286 ekt~~~k~~~~lq~kiq~LekLcRALq~ernel~~~~~~~e~~v~~k~~~~~la~--pe~~-~~~~~~~~~----~~~ts  358 (391)
T KOG1850|consen  286 EKTVRDKEYETLQKKIQRLEKLCRALQTERNELNKKLEDLEAQVSAKNAMKDLAT--PESK-PCIILDSEK----KLNTS  358 (391)
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHhcccchhhhhhhhcC--cccc-ccccccchh----ccCCc
Confidence            3344444555556788899999998864422    11111  1111  1111222  2211 222 12221    22333


Q ss_pred             CCCCCCCCCCCcCccccCCCCCCcccCCCCCC
Q 022126          217 SPGTPGPREDIWPARQNSSNSGPFDIATGSPA  248 (302)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  248 (302)
                      +-.++|+--+|=|--..+-+.||-  ++|||.
T Consensus       359 ~~~a~a~~~~gep~~e~s~~~~~~--e~~sa~  388 (391)
T KOG1850|consen  359 SKRAAASHLEGEPKQESSATEKPA--ETGSAG  388 (391)
T ss_pred             hhcccccCCCCCccchhhhccCCC--CCCCcc
Confidence            345588888888988888888985  455654

>PRK04325 hypothetical protein; Provisional

Probab=88.46  E-value=7.1  Score=30.12  Aligned_cols=34  Identities=9%  Similarity=0.067  Sum_probs=15.1

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          144 SKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYES  177 (302)
Q Consensus       144 rKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~  177 (302)
                      ...+++|.+...+-.+++.+|+.....|..++..
T Consensus        22 E~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl~~   55 (74)
T PRK04325         22 EDLIDGLNATVARQQQTLDLLQAQLRLLYQQMRD   55 (74)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444444444444333

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=88.45  E-value=10  Score=32.63  Aligned_cols=13  Identities=23%  Similarity=0.401  Sum_probs=10.6

Q ss_pred             HHHhcCCChHHHH
Q 022126           63 NMAMAGVSPQILM   75 (302)
Q Consensus        63 t~vL~GlsP~~Im   75 (302)
                      +.-|.|++-++|+
T Consensus        38 Nr~LrG~~reEVv   50 (135)
T KOG4196|consen   38 NRHLRGLSREEVV   50 (135)
T ss_pred             HHHhcCCCHHHHH
Confidence            4468899999988

>KOG0243 consensus Kinesin-like protein [Cytoskeleton]

Probab=88.19  E-value=7.9  Score=43.22  Aligned_cols=34  Identities=26%  Similarity=0.459  Sum_probs=15.4

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          141 ESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       141 e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      ..|+++.+.|++++..+++++.-+++.|.+++++
T Consensus       479 ~~l~~~~~~~k~~L~~~~~el~~~~ee~~~~~~~  512 (1041)
T KOG0243|consen  479 ELLKEEKEKLKSKLQNKNKELESLKEELQQAKAT  512 (1041)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444444444433

>KOG3002 consensus Zn finger protein [General function prediction only]

Probab=88.05  E-value=0.37  Score=46.55  Aligned_cols=42  Identities=29%  Similarity=0.787  Sum_probs=34.5

Q ss_pred             CccccCcccccCCcEEecC--CccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTC--GHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~C--GHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      +-|++|+..|.  +=+-.|  ||+-|..|-.+.   ...||.|+-++++
T Consensus        49 leCPvC~~~l~--~Pi~QC~nGHlaCssC~~~~---~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   49 LDCPVCFNPLS--PPIFQCDNGHLACSSCRTKV---SNKCPTCRLPIGN   92 (299)
T ss_pred             ccCchhhccCc--ccceecCCCcEehhhhhhhh---cccCCcccccccc
Confidence            46999999996  336777  999999998653   6789999998873

>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others

Probab=87.98  E-value=12  Score=31.73  Aligned_cols=6  Identities=17%  Similarity=-0.230  Sum_probs=1.8

Q ss_pred             hhhhhh
Q 022126           84 FYLGQK   89 (302)
Q Consensus        84 Fw~~Q~   89 (302)
                      |...+.
T Consensus        21 ~Vd~~~   26 (158)
T PF03938_consen   21 VVDVDK   26 (158)
T ss_dssp             EE-HHH
T ss_pred             EeeHHH
Confidence            333333

OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=87.73  E-value=2.2  Score=43.75  Aligned_cols=57  Identities=16%  Similarity=0.303  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      ++.+.+...++|++++++++.|++.+.++.+++++++++...++++|++-.+.++.+
T Consensus        70 ALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~~  126 (475)
T PRK13729         70 ATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGAN  126 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcC
Confidence            334444445556667777778888888888888888888888888888777777766

>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]

Probab=87.54  E-value=0.16  Score=53.74  Aligned_cols=46  Identities=20%  Similarity=0.562  Sum_probs=37.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc--C-CCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS--N-DAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~--~-~~~CPvC~~~l~~   47 (302)
                      +.|+||..... .++.+.|-|+||..|+...|.  + ...||+|+....+
T Consensus        22 lEc~ic~~~~~-~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK   70 (684)
T KOG4362|consen   22 LECPICLEHVK-EPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK   70 (684)
T ss_pred             ccCCceeEEee-ccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence            46999998876 578999999999999998764  3 6789999966543

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=87.42  E-value=14  Score=32.30  Aligned_cols=67  Identities=18%  Similarity=0.378  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          112 QEKFTEKLEQVHTAYQKMAKRCQMM-------EQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       112 ~~~l~~ki~e~~s~~~kl~~kl~~m-------e~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      ...|.++|++-+.++.+|+.++..-       ...+..+..++..+...+.++.....++.+....++.+.+.+
T Consensus        51 n~~l~~kIeERn~eL~~Lk~~~~~~v~~L~h~keKl~~~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~  124 (177)
T PF13870_consen   51 NQQLNEKIEERNKELLKLKKKIGKTVQILTHVKEKLHFLSEELERLKQELKDREEELAKLREELYRVKKERDKL  124 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455566666666666665544322       222333333333444444444444444444444444443333

>KOG3859 consensus Septins (P-loop GTPases) [Cell cycle control, cell division, chromosome partitioning]

Probab=87.38  E-value=17  Score=35.68  Aligned_cols=68  Identities=19%  Similarity=0.405  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          101 VAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       101 ~~~lreK~e~L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      +..+..|.+.|.+.+-+++.+.++.+++..+   ++-..-+.|++..+|=..+++||.|   +|++-++.+.++
T Consensus       332 ~~e~qrkEee~rqmFvqrvkekE~elke~Ek---el~~kf~~lkr~h~eEk~kle~~rr---~Leee~~~f~~r  399 (406)
T KOG3859|consen  332 LGELQRKEEEMRQMFVQRVKEKEAELKEAEK---ELHEKFDRLKRLHQEEKKKLEEKRK---QLEEEVNAFQRR  399 (406)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHH
Confidence            3445555555666666666666666655544   2333346666666666677776654   566677776555

>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]

Probab=87.35  E-value=22  Score=34.08  Aligned_cols=9  Identities=11%  Similarity=0.139  Sum_probs=4.2

Q ss_pred             CCCCCCCCC
Q 022126          244 TGSPAKQPV  252 (302)
Q Consensus       244 ~~~~~~~~~  252 (302)
                      +|+|-|.+|
T Consensus       237 g~~pltp~a  245 (333)
T KOG1853|consen  237 GDVPLTPDA  245 (333)
T ss_pred             CCCCCCchh
Confidence            345555444

>TIGR01069 mutS2 MutS2 family protein

Probab=87.35  E-value=11  Score=40.87  Aligned_cols=12  Identities=25%  Similarity=0.304  Sum_probs=6.4

Q ss_pred             hHhhhhhCcCCC
Q 022126          278 TLRNLILSPIKR  289 (302)
Q Consensus       278 ~~~~~~~~~~~~  289 (302)
                      +||..|-.=+++
T Consensus       735 ~Lr~~v~~~L~~  746 (771)
T TIGR01069       735 KLRKGVQELLKN  746 (771)
T ss_pred             HHHHHHHHHhcC
Confidence            466655544444

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

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

Probab=87.33  E-value=16  Score=30.47  Aligned_cols=56  Identities=18%  Similarity=0.173  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       121 e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      ++-++-+.|...+..++.+.++..+.+.||+.++.|--+....-...|..|..++.
T Consensus        34 eL~kqkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le~eK~ak~~l~~r~~   89 (107)
T PF09304_consen   34 ELAKQKDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLEDEKQAKLELESRLL   89 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444455555666677777777777777777777766655554444555555544

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.

>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]

Probab=87.30  E-value=21  Score=39.24  Aligned_cols=14  Identities=36%  Similarity=0.954  Sum_probs=11.0

Q ss_pred             CCCCCCCccccccC
Q 022126           35 DAACPICDQVLSKS   48 (302)
Q Consensus        35 ~~~CPvC~~~l~~~   48 (302)
                      ...||+|++++...
T Consensus       457 ~~~CPvCg~~l~~~  470 (908)
T COG0419         457 GEKCPVCGQELPEE  470 (908)
T ss_pred             CCCCCCCCCCCCcH
Confidence            57899999887653

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

Probab=87.24  E-value=8.7  Score=40.59  Aligned_cols=34  Identities=32%  Similarity=0.557  Sum_probs=21.9

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          145 KDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       145 Kkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      .++.++.++.++..-+.++-+++|.+|+.+|+.+
T Consensus       447 ~~ik~~r~~~k~~~~e~~~Kee~~~qL~~e~e~~  480 (594)
T PF05667_consen  447 QEIKELREEIKEIEEEIRQKEELYKQLVKELEKL  480 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            4444555556666666677777777777776654

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

Probab=87.17  E-value=2.1  Score=40.34  Aligned_cols=38  Identities=24%  Similarity=0.406  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 022126          115 FTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQE  152 (302)
Q Consensus       115 l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~  152 (302)
                      |+.++.+++.++.++..++.+++.|++.|+++|..|-|
T Consensus        91 FR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYE  128 (248)
T PF08172_consen   91 FRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYE  128 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44566677777777888888999999999999888743

These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane

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

Probab=87.02  E-value=15  Score=36.51  Aligned_cols=63  Identities=14%  Similarity=0.294  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          112 QEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       112 ~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      ...+++...++...++++..+=.-+..+++.+..+..+++..|.+-..++++..+....+-.+
T Consensus       240 ~~~L~kl~~~i~~~lekI~sREk~iN~qle~l~~eYr~~~~~ls~~~~~y~~~s~~V~~~t~~  302 (359)
T PF10498_consen  240 KSQLDKLQQDISKTLEKIESREKYINNQLEPLIQEYRSAQDELSEVQEKYKQASEGVSERTRE  302 (359)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence            334444444444455555555555666666666666666666666666666655554444433

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

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

Probab=87.02  E-value=18  Score=37.89  Aligned_cols=32  Identities=28%  Similarity=0.342  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 022126          133 CQMMEQEIESLSKDKQELQEKFSEKSRQKRKL  164 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky~EKsRq~~qL  164 (302)
                      ..++...+..|+.++..|..+..|..+...++
T Consensus       215 ~~e~~~ri~~LEedi~~l~qk~~E~e~~~~~l  246 (546)
T PF07888_consen  215 LAEARQRIRELEEDIKTLTQKEKEQEKELDKL  246 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333344444444444444444443333333

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 [].

>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs

Probab=87.00  E-value=23  Score=38.31  Aligned_cols=16  Identities=19%  Similarity=0.385  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHHH
Q 022126          161 KRKLDEMYDQLRSEYE  176 (302)
Q Consensus       161 ~~qLqelYdkLK~~~e  176 (302)
                      ++.|+.-.+++|.+.+
T Consensus       648 l~~l~~si~~lk~k~~  663 (717)
T PF10168_consen  648 LQDLKASIEQLKKKLD  663 (717)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3444444444444443

It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].

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

Probab=86.94  E-value=12  Score=37.71  Aligned_cols=31  Identities=23%  Similarity=0.283  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022126          151 QEKFSEKSRQKRKLDEMYDQLRSEYESMKRS  181 (302)
Q Consensus       151 q~ky~EKsRq~~qLqelYdkLK~~~e~~~rs  181 (302)
                      +..|.+-.|++.-.+++|+.|..+++.++-+
T Consensus       354 ~~el~~L~Re~~~~~~~Y~~l~~r~eea~~~  384 (498)
T TIGR03007       354 EAELTQLNRDYEVNKSNYEQLLTRRESAEVS  384 (498)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3455667778888888999999898877644

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.

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.90  E-value=0.3  Score=34.91  Aligned_cols=43  Identities=26%  Similarity=0.684  Sum_probs=19.2

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhh-----cCCCCCCCCccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKIL-----SNDAACPICDQV   44 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~-----~~~~~CPvC~~~   44 (302)
                      |.|++....+..-+=...|.|+-|.+ +..++     .....||+|+++
T Consensus         3 L~CPls~~~i~~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRIPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SSEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEeCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            57999888886433367799998754 22222     235689999874

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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

>PF09728 Taxilin: Myosin-like coiled-coil protein; InterPro: IPR019132 Taxilin contains an extraordinarily long coiled-coil domain in its C-terminal half and is ubiquitously expressed

Probab=86.88  E-value=31  Score=33.41  Aligned_cols=76  Identities=18%  Similarity=0.368  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          103 QCRQKCEAMQEKFTE---KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       103 ~lreK~e~L~~~l~~---ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      .+.+|++..+..+.+   ....+..+|+++.+++..++.|...++++.+.-...+-+=.-+...+.+-|+.++.+.+++
T Consensus       220 ~Y~~Kf~efq~tL~kSNe~F~tfk~Emekm~Kk~kklEKE~~~~k~k~e~~n~~l~~m~eer~~~~~~~~~~~~k~~kL  298 (309)
T PF09728_consen  220 LYSEKFEEFQDTLNKSNEVFETFKKEMEKMSKKIKKLEKENQTWKSKWEKSNKALIEMAEERQKLEKELEKLKKKIEKL  298 (309)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555543   3334455666666666666666666666665555555444445555555566666655544

It is a novel binding partner of several syntaxin family members and is possibly involved in Ca(2+)-dependent exocytosis in neuroendocrine cells []. Gamma-taxilin, described as leucine zipper protein Factor Inhibiting ATF4-mediated Transcription (FIAT), localises to the nucleus in osteoblasts and dimerises with ATF4 to form inactive dimers, thus inhibiting ATF4-mediated transcription [].

>PF03148 Tektin: Tektin family; InterPro: IPR000435 Tektin heteropolymers form unique protofilaments of flagellar microtubules []

Probab=86.86  E-value=35  Score=33.92  Aligned_cols=52  Identities=15%  Similarity=0.344  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 022126          107 KCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKS  158 (302)
Q Consensus       107 K~e~L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKs  158 (302)
                      .....+..|.+++++...+.++|+..+..+..|+..+++.+..|.+...+|.
T Consensus       241 Q~~~vn~al~~Ri~et~~ak~~Le~ql~~~~~ei~~~e~~i~~L~~ai~~k~  292 (384)
T PF03148_consen  241 QADAVNAALRKRIHETQEAKNELEWQLKKTLQEIAEMEKNIEDLEKAIRDKE  292 (384)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344455555666666666666655555555666666666666666555554

The proteins are predicted to form extended rods composed of 2 alpha- helical segments (~180 residues long) capable of forming coiled coils, interrupted by non-helical linkers []. The 2 segments are similar in sequence, indicating a gene duplication event. Along each tektin rod, cysteine residues occur with a periodicity of ~8nm, coincident with the axial repeat of tubulin dimers in microtubules []. It is proposed that the assembly of tektin heteropolymers produces filaments with repeats of 8, 16, 24, 32, 40, 48 and 96nm, generating the basis for the complex spatial arrangements of axonemal components [].; GO: 0000226 microtubule cytoskeleton organization, 0005874 microtubule

>PRK02119 hypothetical protein; Provisional

Probab=86.84  E-value=9.1  Score=29.45  Aligned_cols=26  Identities=15%  Similarity=0.185  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          149 ELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       149 ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      +|.+...+-.+++..|+.....|+.+
T Consensus        27 ~LN~~v~~Qq~~id~L~~ql~~L~~r   52 (73)
T PRK02119         27 ELNQALIEQQFVIDKMQVQLRYMANK   52 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333344444

>PF10205 KLRAQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019343 This entry represents a N-terminal 100 residues long domain, which contains a conserved KLRAQ motif

Probab=86.83  E-value=7.8  Score=32.01  Aligned_cols=53  Identities=25%  Similarity=0.399  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          124 TAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       124 s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      ++|.+|..+..-++.-+=..+.++.+|.+.+.+|.-.+++++.-.|.|--+..
T Consensus         5 ~eYsKLraQ~~vLKKaVieEQ~k~~~L~e~Lk~ke~~LRk~eqE~dSL~FrN~   57 (102)
T PF10205_consen    5 QEYSKLRAQNQVLKKAVIEEQAKNAELKEQLKEKEQALRKLEQENDSLTFRNQ   57 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555555555555555666666666666666666666666666654443

This domain is found in a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. These proteins also contain a C-terminal TTKRSYEDQ motif domain (IPR019348 from INTERPRO). The function of these proteins is not known.

>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]

Probab=86.78  E-value=8.2  Score=43.75  Aligned_cols=44  Identities=23%  Similarity=0.429  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHH
Q 022126          135 MMEQEIESLSKDKQELQEKFSEKSRQKRKLD-----EMYDQLRSEYESM  178 (302)
Q Consensus       135 ~me~E~e~LrKkn~ELq~ky~EKsRq~~qLq-----elYdkLK~~~e~~  178 (302)
                      ...++++.|+++..-|...|+|...+..+|+     +.||.++.-+++.
T Consensus      1264 ~a~~~LesLq~~~~~l~~~~keL~e~~~~ik~sdi~GA~~~~r~a~~~s 1312 (1758)
T KOG0994|consen 1264 LAGKDLESLQREFNGLLTTYKELREQLEKIKESDILGAFNSTRHAYEQS 1312 (1758)
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccCchhHHHHHHHHHHHH
Confidence            3457888888888888888888887777765     4788888887743

>PRK09039 hypothetical protein; Validated

Probab=86.70  E-value=9.6  Score=37.37  Aligned_cols=56  Identities=11%  Similarity=0.250  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          123 HTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       123 ~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      .+.|.....++..++++++.||+.+..|+..+.+-..+....+.-++.|+++++.+
T Consensus       129 k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a  184 (343)
T PRK09039        129 KQVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVA  184 (343)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333334444555555555555555555555555555555555555555554433

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=86.52  E-value=5.8  Score=40.71  Aligned_cols=20  Identities=20%  Similarity=0.451  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 022126          158 SRQKRKLDEMYDQLRSEYES  177 (302)
Q Consensus       158 sRq~~qLqelYdkLK~~~e~  177 (302)
                      ..+.++++.+.+.|.++++.
T Consensus       122 ~~~~~~~~~~l~~l~~~l~~  141 (472)
T TIGR03752       122 KSERQQLQGLIDQLQRRLAG  141 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHhh
Confidence            44566788888888888653

Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.

>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=86.45  E-value=6.2  Score=34.53  Aligned_cols=17  Identities=41%  Similarity=0.433  Sum_probs=7.3

Q ss_pred             HHHHHHHhHHHHHHHHH
Q 022126          139 EIESLSKDKQELQEKFS  155 (302)
Q Consensus       139 E~e~LrKkn~ELq~ky~  155 (302)
                      ..+.|++++.+|+.+|.
T Consensus        52 d~eeLk~~i~~lq~~~~   68 (155)
T PF06810_consen   52 DNEELKKQIEELQAKNK   68 (155)
T ss_pred             CHHHHHHHHHHHHHHHH
Confidence            33444444444444444

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

>COG4372 Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]

Probab=86.44  E-value=35  Score=34.64  Aligned_cols=34  Identities=29%  Similarity=0.495  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 022126          133 CQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDE  166 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqe  166 (302)
                      +.....++..+.+..+.|+..+..-+-|++||.+
T Consensus       132 ~~kAqQ~lar~t~Q~q~lqtrl~~l~~qr~ql~a  165 (499)
T COG4372         132 LAKAQQELARLTKQAQDLQTRLKTLAEQRRQLEA  165 (499)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555556666555544444444433

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

Probab=86.43  E-value=10  Score=33.86  Aligned_cols=42  Identities=24%  Similarity=0.232  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          133 CQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      +.+.+..++.++.++.-|+-.|.--..+.++|+.-++.|..+
T Consensus       139 l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l~~En~~Lv~R  180 (194)
T PF08614_consen  139 LKEKNKANEILQDELQALQLQLNMLEEKLRKLEEENRELVER  180 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333334444444444444444444455555555555555544

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.

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

Probab=86.35  E-value=7  Score=31.99  Aligned_cols=52  Identities=19%  Similarity=0.325  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHH--HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          124 TAYQKMAKRCQMMEQEIESL--SKDKQELQEKFSEKSRQKRKLDEMYDQLRSEY  175 (302)
Q Consensus       124 s~~~kl~~kl~~me~E~e~L--rKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~  175 (302)
                      ..++....+++.+|.+++.|  +++.++|+-...+=+.+...|.+-++.+.+..
T Consensus        42 ~~~~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~~~~   95 (106)
T PF10805_consen   42 ERLDEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVSHQL   95 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            33334444555555555555  55555555555555555555555555554443

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

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

Probab=86.26  E-value=4.6  Score=30.55  Aligned_cols=36  Identities=22%  Similarity=0.376  Sum_probs=16.2

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          144 SKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMK  179 (302)
Q Consensus       144 rKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~  179 (302)
                      ...+++|.+...+-.+++.+|+..+..|..++..+.
T Consensus        17 e~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   52 (69)
T PF04102_consen   17 EDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELE   52 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            334444444444445555555555556666644443

It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.

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

Probab=86.24  E-value=22  Score=32.80  Aligned_cols=6  Identities=67%  Similarity=1.929  Sum_probs=4.6

Q ss_pred             CCCCCc
Q 022126           37 ACPICD   42 (302)
Q Consensus        37 ~CPvC~   42 (302)
                      .||+|+
T Consensus         1 ~C~iC~    6 (302)
T PF10186_consen    1 QCPICH    6 (302)
T ss_pred             CCCCCC
Confidence            488888

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

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=86.11  E-value=0.15  Score=39.30  Aligned_cols=41  Identities=34%  Similarity=0.632  Sum_probs=24.9

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      +.|+.|..+|.-   ..  ||.+|..|-..+ .....||-|+.+|..
T Consensus         2 ~~CP~C~~~L~~---~~--~~~~C~~C~~~~-~~~a~CPdC~~~Le~   42 (70)
T PF07191_consen    2 NTCPKCQQELEW---QG--GHYHCEACQKDY-KKEAFCPDCGQPLEV   42 (70)
T ss_dssp             -B-SSS-SBEEE---ET--TEEEETTT--EE-EEEEE-TTT-SB-EE
T ss_pred             CcCCCCCCccEE---eC--CEEECccccccc-eecccCCCcccHHHH
Confidence            479999998841   22  999999997754 456789999998853

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

>PF08581 Tup_N: Tup N-terminal; InterPro: IPR013890 The N-terminal region of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor []

Probab=86.03  E-value=15  Score=28.87  Aligned_cols=21  Identities=19%  Similarity=0.276  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHHHHHhHHHH
Q 022126          130 AKRCQMMEQEIESLSKDKQEL  150 (302)
Q Consensus       130 ~~kl~~me~E~e~LrKkn~EL  150 (302)
                      ..+++..-.|++.+|.++.||
T Consensus        31 e~ki~~Qi~Em~~ir~~v~eL   51 (79)
T PF08581_consen   31 EHKINSQIQEMQQIRQKVYEL   51 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333444444445555555444

; PDB: 3VP9_B 3VP8_B.

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

Probab=86.01  E-value=22  Score=30.84  Aligned_cols=59  Identities=15%  Similarity=0.393  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          115 FTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRS  173 (302)
Q Consensus       115 l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~  173 (302)
                      .+..+..+..+++.+...+..++.++++++.++.+|-..+.++..+...|..+-..+.+
T Consensus        50 ~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv~eLE~~~~~~~~  108 (140)
T PF10473_consen   50 SKAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKKQEKVSELESLNSSLEN  108 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence            33455566667777777778888888888888888888888887777777766555443

There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding

>PRK02793 phi X174 lysis protein; Provisional

Probab=85.96  E-value=11  Score=28.95  Aligned_cols=33  Identities=15%  Similarity=0.209  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          147 KQELQEKFSEKSRQKRKLDEMYDQLRSEYESMK  179 (302)
Q Consensus       147 n~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~  179 (302)
                      +++|.+...+-.+++..|+.....|+.++..+.
T Consensus        24 Ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   56 (72)
T PRK02793         24 IEELNVTVTAHEMEMAKLRDHLRLLTEKLKASQ   56 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            333433344334444444444444444443333

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

Probab=85.80  E-value=6.6  Score=38.25  Aligned_cols=59  Identities=24%  Similarity=0.442  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          116 TEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       116 ~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      .+.+.+.+..+..+..++..++.+.+...++.++|+.....-.+++..-+.|.+.|..+
T Consensus       234 ~~~L~~~~~~l~~l~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~kl~rA~~Li~~L~~E  292 (344)
T PF12777_consen  234 EEQLAEKQAELAELEEKLAALQKEYEEAQKEKQELEEEIEETERKLERAEKLISGLSGE  292 (344)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHhhhcch
Confidence            34555666666777777777777777777777788777777777777777777666544

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

>PF10392 COG5: Golgi transport complex subunit 5; InterPro: IPR019465 The conserved oligomeric Golgi (COG) complex is a peripheral membrane complex involved in intra-Golgi protein trafficking

Probab=85.73  E-value=20  Score=30.13  Aligned_cols=55  Identities=24%  Similarity=0.308  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          120 EQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       120 ~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      .+++..++.++..+..+....+.|++++.|=-++......++.+++.-.+-||+=
T Consensus        68 ~~~~~~l~~v~~~v~~L~~s~~RL~~eV~~Py~~~~~~~~~L~rl~~t~~LLR~~  122 (132)
T PF10392_consen   68 EELESVLQAVRSSVESLQSSYERLRSEVIEPYEKIQKLTSQLERLHQTSDLLRSV  122 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455566666667777777778888877777777777777777777777777653

Subunit 5 is located in the smaller, B lobe, together with subunits 6-8, and has been shown to bind subunits 1 and 7 [].

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

Probab=85.69  E-value=17  Score=34.19  Aligned_cols=58  Identities=14%  Similarity=0.304  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEY  175 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~  175 (302)
                      .+..++.+++.++.+..+++.++..+..+.++|++...+...++.+++....-.+..+
T Consensus        90 e~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l~~~~~~~e~~~~e~~~~~  147 (239)
T COG1579          90 ELRALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLERLEKNLAEAEARL  147 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555556666666666666666666666666666666666655555554444443

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

Probab=85.61  E-value=33  Score=33.08  Aligned_cols=11  Identities=27%  Similarity=0.564  Sum_probs=5.4

Q ss_pred             HhhhhhCcCCC
Q 022126          279 LRNLILSPIKR  289 (302)
Q Consensus       279 ~~~~~~~~~~~  289 (302)
                      |=.+||+|+.+
T Consensus       404 ~~~~~l~~~~~  414 (423)
T TIGR01843       404 VIEYLLKPITD  414 (423)
T ss_pred             HHHHHHHHHHH
Confidence            34455555543

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.

>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length

Probab=85.60  E-value=0.5  Score=40.72  Aligned_cols=31  Identities=16%  Similarity=0.636  Sum_probs=25.5

Q ss_pred             CccccCcccccC--CcEEecCC------ccccHHHHHhh
Q 022126            1 MRCNACWRELEG--RAISTTCG------HLLCTEDANKI   31 (302)
Q Consensus         1 l~CNiC~~~l~~--~~vvT~CG------HiFC~~Ci~~~   31 (302)
                      +.|-||...+.+  ..|..+||      |.||.+|+.+|
T Consensus        27 ~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw   65 (134)
T PF05883_consen   27 VECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRW   65 (134)
T ss_pred             eeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHH
Confidence            358999999865  56666776      89999999998

The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.

>PRK02224 chromosome segregation protein; Provisional

Probab=85.45  E-value=49  Score=35.81  Aligned_cols=15  Identities=7%  Similarity=-0.037  Sum_probs=6.6

Q ss_pred             ChHHHHHHHHHhhhh
Q 022126           70 SPQILMKSAYRSVMF   84 (302)
Q Consensus        70 sP~~Ime~a~RAi~F   84 (302)
                      +|....++..+++..
T Consensus       147 ~p~~R~~ii~~l~~l  161 (880)
T PRK02224        147 TPSDRQDMIDDLLQL  161 (880)
T ss_pred             CHHHHHHHHHHHhCC
Confidence            444433444444444

>KOG4367 consensus Predicted Zn-finger protein [Function unknown]

Probab=85.19  E-value=4.4  Score=41.43  Aligned_cols=148  Identities=14%  Similarity=0.182  Sum_probs=74.8

Q ss_pred             ccccHHHHHhhhcCCCCCCCCccccccC--CCcccccCCChHHHHHHhcCCChHHHHHHHHH---hhhhhhhhhHHHHHH
Q 022126           21 HLLCTEDANKILSNDAACPICDQVLSKS--LMKPVDINPNDEWVNMAMAGVSPQILMKSAYR---SVMFYLGQKELEMQY   95 (302)
Q Consensus        21 HiFC~~Ci~~~~~~~~~CPvC~~~l~~~--div~~~LnPse~~Kt~vL~GlsP~~Ime~a~R---Ai~Fw~~Q~~qe~~y   95 (302)
                      -+||..|      ....|--|+..+...  .+..-.|-|..+-  .|-..++|-.++.++-+   ...+|.-|-+..+.|
T Consensus       176 ~v~ceqc------dv~yc~pc~~~~hp~rgplakh~l~~~~~g--rvs~~~s~r~~~~ct~h~~e~~smyc~~ck~pvc~  247 (699)
T KOG4367|consen  176 TVMCEQC------DVFYCDPCRLRCHPPRGPLAKHRLVPPAQG--RVSRRLSPRKVSTCTDHELENHSMYCVQCKMPVCY  247 (699)
T ss_pred             hhhHhhC------ceEEechHHhccCCCCCchhhcccCCcccC--ceeeccchhhhhhccCCCCCCceEEEEecCChHHH
Confidence            3555555      344566666665332  2222233333332  25556677777766544   345677777777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q 022126           96 KMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSE-KSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus        96 Q~~~l~~~lreK~e~L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~E-KsRq~~qLqelYdkLK~~  174 (302)
                      |--.-.+...-....|....+-.-.++.++++.|..|..+.+.++-+||.-.+-+|+.-.| ++-=..|...|+|.|.++
T Consensus       248 ~clee~khs~hevkal~~~~k~hksqls~al~~lsdrak~a~e~l~~lr~m~~~iq~n~~ef~a~l~~q~d~lid~l~~r  327 (699)
T KOG4367|consen  248 QCLEEGKHSSHEVKALGAMWKLHKSQLSQALNGLSDRAKEAKEFLVQLRNMVQQIQENSVEFEACLVAQCDALIDALNRR  327 (699)
T ss_pred             HHHHhhcccchhhhhHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHH
Confidence            6100000000011223333333334566666666666666666666666666666555444 233345666666666444


Q ss_pred             HH
Q 022126          175 YE  176 (302)
Q Consensus       175 ~e  176 (302)
                      -+
T Consensus       328 k~  329 (699)
T KOG4367|consen  328 KA  329 (699)
T ss_pred             HH
Confidence            44

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=85.18  E-value=7.5  Score=41.06  Aligned_cols=60  Identities=18%  Similarity=0.305  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022126          122 VHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRS  181 (302)
Q Consensus       122 ~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rs  181 (302)
                      +.-++.+++.|-++++.|++.+..|++||++.+..|.-++.+|.+...+-.++++.+|..
T Consensus        91 Vs~EL~ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El~~~  150 (907)
T KOG2264|consen   91 VSLELTELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEELRET  150 (907)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHHHhh
Confidence            334444555556667777777778888888777777777777777777776666655543

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

Probab=85.16  E-value=21  Score=30.10  Aligned_cols=20  Identities=25%  Similarity=0.418  Sum_probs=7.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 022126          149 ELQEKFSEKSRQKRKLDEMY  168 (302)
Q Consensus       149 ELq~ky~EKsRq~~qLqelY  168 (302)
                      +|...+.+...+|.-+=+||
T Consensus        72 ~L~~el~~l~~ry~t~Lell   91 (120)
T PF12325_consen   72 ELEQELEELQQRYQTLLELL   91 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHh
Confidence            33333333333333333333

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

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

Probab=85.01  E-value=22  Score=32.15  Aligned_cols=63  Identities=21%  Similarity=0.344  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR  180 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~r  180 (302)
                      ++.+.+...+++..++.+++..+..|++..+-+..+-+++..+..+++.--+.++..++.++.
T Consensus       118 ~~~~~~~~~~~~e~~i~~Le~ki~el~~~~~~~~~~ke~~~~ei~~lks~~~~l~~~~~~~e~  180 (190)
T PF05266_consen  118 KIEEKEAELKELESEIKELEMKILELQRQAAKLKEKKEAKDKEISRLKSEAEALKEEIENAEL  180 (190)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333344444445555555555555555555556666777777777777777777665543

>TIGR00606 rad50 rad50

Probab=84.96  E-value=31  Score=39.55  Aligned_cols=16  Identities=31%  Similarity=0.980  Sum_probs=12.4

Q ss_pred             CCCCCCCCccccccCC
Q 022126           34 NDAACPICDQVLSKSL   49 (302)
Q Consensus        34 ~~~~CPvC~~~l~~~d   49 (302)
                      ....||+|.+.|....
T Consensus       676 ~~~~C~LC~R~f~~ee  691 (1311)
T TIGR00606       676 NQSCCPVCQRVFQTEA  691 (1311)
T ss_pred             cCCcCCCCCCCCCChh
Confidence            3568999999997643

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

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

Probab=84.93  E-value=34  Score=33.08  Aligned_cols=67  Identities=22%  Similarity=0.357  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH-------HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHH
Q 022126          115 FTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQ-------EKFSEKSRQKRKLDEMY-------DQLRSEYESMKR  180 (302)
Q Consensus       115 l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq-------~ky~EKsRq~~qLqelY-------dkLK~~~e~~~r  180 (302)
                      ...++..+-+....|..||+.-+.|++.++|..+-||       ..|++-..+++||=+.|       +-||++++-..|
T Consensus       124 ~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRle~LqsiRP~~MdEyE~~EeeLqkly~~Y~l~f~nl~yL~~qldd~~r  203 (338)
T KOG3647|consen  124 SRAQLNNVASDEAALGSKIERRKAELERTRKRLEALQSIRPAHMDEYEDCEEELQKLYQRYFLRFHNLDYLKSQLDDRTR  203 (338)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhh
Confidence            3345555555555566777788888899999888888       35665555555555444       346666664433


Q ss_pred             h
Q 022126          181 S  181 (302)
Q Consensus       181 s  181 (302)
                      |
T Consensus       204 s  204 (338)
T KOG3647|consen  204 S  204 (338)
T ss_pred             h
Confidence            3

>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=84.84  E-value=25  Score=32.62  Aligned_cols=53  Identities=9%  Similarity=0.264  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 022126          115 FTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEM  167 (302)
Q Consensus       115 l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqel  167 (302)
                      +...+..++.+++.++...+.++..+++++++..+|++..++-..-.+.|..+
T Consensus        54 L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~~~~~~~~~l~p~  106 (251)
T PF11932_consen   54 LLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIEQIEETRQELVPL  106 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444555555555555555566666666666666666666555555555443

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.

>PRK11546 zraP zinc resistance protein; Provisional

Probab=84.71  E-value=11  Score=32.85  Aligned_cols=38  Identities=13%  Similarity=0.125  Sum_probs=17.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126           88 QKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTA  125 (302)
Q Consensus        88 Q~~qe~~yQ~~~l~~~lreK~e~L~~~l~~ki~e~~s~  125 (302)
                      |.+.|.+-+...|.+.+..+...|-+++-.|-.|+++.
T Consensus        43 ~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnAL   80 (143)
T PRK11546         43 PLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNAL   80 (143)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35555444433455455544444444444444444443

>PF10158 LOH1CR12: Tumour suppressor protein; InterPro: IPR018780 This entry represents a region of 130 amino acids that is the most conserved part of some hypothetical proteins involved in loss of heterozygosity, and thus, tumour suppression []

Probab=84.70  E-value=18  Score=30.99  Aligned_cols=18  Identities=6%  Similarity=0.159  Sum_probs=14.0

Q ss_pred             HhcCCChHHHHHHHHHhh
Q 022126           65 AMAGVSPQILMKSAYRSV   82 (302)
Q Consensus        65 vL~GlsP~~Ime~a~RAi   82 (302)
                      ++.++++.-++..|+|-.
T Consensus        20 ~leklds~~~l~Lc~R~Q   37 (131)
T PF10158_consen   20 VLEKLDSRPVLRLCSRYQ   37 (131)
T ss_pred             HHHccChHHHHHHHHHHH
Confidence            788888888887777653

The exact function of these proteins is not known.

>PRK04406 hypothetical protein; Provisional

Probab=84.62  E-value=12  Score=29.06  Aligned_cols=26  Identities=19%  Similarity=0.250  Sum_probs=10.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhH
Q 022126          122 VHTAYQKMAKRCQMMEQEIESLSKDK  147 (302)
Q Consensus       122 ~~s~~~kl~~kl~~me~E~e~LrKkn  147 (302)
                      ++..+..|..++.-++.-++.|.+.+
T Consensus         9 le~Ri~~LE~~lAfQE~tIe~LN~~v   34 (75)
T PRK04406          9 LEERINDLECQLAFQEQTIEELNDAL   34 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444444444444443333

>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]

Probab=84.53  E-value=0.61  Score=38.68  Aligned_cols=29  Identities=17%  Similarity=0.387  Sum_probs=26.4

Q ss_pred             EecCCccccHHHHHhhhcCCCCCCCCccc
Q 022126           16 STTCGHLLCTEDANKILSNDAACPICDQV   44 (302)
Q Consensus        16 vT~CGHiFC~~Ci~~~~~~~~~CPvC~~~   44 (302)
                      =-.|.|.|=..||.+|++....||.|.+.
T Consensus        78 WG~CNHaFH~hCisrWlktr~vCPLdn~e  106 (114)
T KOG2930|consen   78 WGVCNHAFHFHCISRWLKTRNVCPLDNKE  106 (114)
T ss_pred             eeecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence            45799999999999999999999999875

>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=84.47  E-value=28  Score=32.48  Aligned_cols=46  Identities=22%  Similarity=0.376  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          130 AKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEY  175 (302)
Q Consensus       130 ~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~  175 (302)
                      +..+..|+..+.+.+.+....++....+-.+|..|.+-.|.++.++
T Consensus        59 ~~DIn~lE~iIkqa~~er~~~~~~i~r~~eey~~Lk~~in~~R~e~  104 (230)
T PF10146_consen   59 NQDINTLENIIKQAESERNKRQEKIQRLYEEYKPLKDEINELRKEY  104 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555555555555567788888888888883

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.

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=84.46  E-value=18  Score=39.38  Aligned_cols=11  Identities=27%  Similarity=0.277  Sum_probs=6.4

Q ss_pred             hHhhhhhCcCC
Q 022126          278 TLRNLILSPIK  288 (302)
Q Consensus       278 ~~~~~~~~~~~  288 (302)
                      .||+.|..=++
T Consensus       746 ~Lr~~v~~~L~  756 (782)
T PRK00409        746 KLRKGVQEFLK  756 (782)
T ss_pred             HHHHHHHHHHc
Confidence            66666655444

>PF13942 Lipoprotein_20: YfhG lipoprotein

Probab=84.44  E-value=7.7  Score=34.93  Aligned_cols=51  Identities=25%  Similarity=0.458  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          120 EQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRS  173 (302)
Q Consensus       120 ~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~  173 (302)
                      .+-.+.|.+|+   ++..+++|.|+.....|+..+.+-+||+..|+..=.+|-+
T Consensus       115 ~eEr~Ry~rLQ---qssD~~lD~Lr~qq~~Lq~qL~~T~RKLEnLTDIERQLSS  165 (179)
T PF13942_consen  115 SEERARYQRLQ---QSSDSELDALRQQQQRLQYQLDTTTRKLENLTDIERQLSS  165 (179)
T ss_pred             HHHHHHHHHHH---HhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHhc
Confidence            34455566653   4788899999999999999999999998888866555543

>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=84.37  E-value=0.36  Score=38.02  Aligned_cols=32  Identities=25%  Similarity=0.488  Sum_probs=26.3

Q ss_pred             EEecCCccccHHHHHhhhc---CCCCCCCCccccc
Q 022126           15 ISTTCGHLLCTEDANKILS---NDAACPICDQVLS   46 (302)
Q Consensus        15 vvT~CGHiFC~~Ci~~~~~---~~~~CPvC~~~l~   46 (302)
                      |.-.|.|.|=..||.+|+.   +...||.|+....
T Consensus        47 v~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   47 VWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             HHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            3557999999999999975   3678999998654

>TIGR01005 eps_transp_fam exopolysaccharide transport protein family

Probab=84.33  E-value=19  Score=38.45  Aligned_cols=58  Identities=10%  Similarity=0.205  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022126          125 AYQKMAKRCQMMEQEIESLSKDKQEL---QEKFSEKSRQKRKLDEMYDQLRSEYESMKRSA  182 (302)
Q Consensus       125 ~~~kl~~kl~~me~E~e~LrKkn~EL---q~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa  182 (302)
                      +++.++.+.+.++.+++.++++..++   ...|.+-.|+..-.+++|+.|-.++++++-..
T Consensus       346 ~~~~a~~~~~~L~~~l~~~~~~~~~~~~~~~e~~~L~Re~~~~~~~Y~~ll~r~~e~~~~~  406 (754)
T TIGR01005       346 QADAAQARESQLVSDVNQLKAASAQAGEQQVDLDALQRDAAAKRQLYESYLTNYRQAASRQ  406 (754)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCcHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            33434444444444555554444333   55677788888888999999999988776554

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.

>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional

Probab=84.30  E-value=31  Score=37.04  Aligned_cols=33  Identities=21%  Similarity=0.156  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022126          151 QEKFSEKSRQKRKLDEMYDQLRSEYESMKRSAI  183 (302)
Q Consensus       151 q~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa~  183 (302)
                      +..|.+-.|+..-.+++|+.|-.+.+.+.-+..
T Consensus       369 e~~~~~L~R~~~~~~~lY~~lL~r~~e~~i~~a  401 (726)
T PRK09841        369 QQEVLRLSRDVEAGRAVYLQLLNRQQELSISKS  401 (726)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            345666778888888999998888777766543

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

Probab=84.16  E-value=26  Score=30.15  Aligned_cols=50  Identities=32%  Similarity=0.557  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHH
Q 022126          127 QKMAKRCQMMEQEIESLSKDKQELQEKFSEK-------SRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       127 ~kl~~kl~~me~E~e~LrKkn~ELq~ky~EK-------sRq~~qLqelYdkLK~~~e  176 (302)
                      +.|.++++.|+.+++...+...+..+++++-       .|+.+.|+.--+.+-.+|+
T Consensus        76 E~l~rriq~LEeele~ae~~L~e~~ekl~e~d~~ae~~eRkv~~le~~~~~~E~k~e  132 (143)
T PF12718_consen   76 EQLNRRIQLLEEELEEAEKKLKETTEKLREADVKAEHFERKVKALEQERDQWEEKYE  132 (143)
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhHHHHHHHHH
Confidence            3466677778888888888777777777653       3454444444444444443

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 [].

>PHA01750 hypothetical protein

Probab=83.72  E-value=12  Score=28.75  Aligned_cols=31  Identities=13%  Similarity=0.340  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 022126          123 HTAYQKMAKRCQMMEQEIESLSKDKQELQEK  153 (302)
Q Consensus       123 ~s~~~kl~~kl~~me~E~e~LrKkn~ELq~k  153 (302)
                      ++++++|..++++....++++.+++.|++++
T Consensus        41 ~~ELdNL~~ei~~~kikqDnl~~qv~eik~k   71 (75)
T PHA01750         41 NSELDNLKTEIEELKIKQDELSRQVEEIKRK   71 (75)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Confidence            4445555444444444444444444444443

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

Probab=83.63  E-value=16  Score=27.35  Aligned_cols=35  Identities=20%  Similarity=0.461  Sum_probs=14.3

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          142 SLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       142 ~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      ..+..|..+..++.|-..+.+.|+.-.+.|+.+++
T Consensus        22 kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~e   56 (61)
T PF08826_consen   22 KVKSANLAFESKLQEAEKRNRELEQEIERLKKEME   56 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333444444444444444444444444433

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

>PRK12704 phosphodiesterase; Provisional

Probab=83.63  E-value=59  Score=33.79  Aligned_cols=16  Identities=19%  Similarity=0.100  Sum_probs=8.8

Q ss_pred             cCCCCCcccccccccC
Q 022126          202 MMDNRDPIRKDWSVYS  217 (302)
Q Consensus       202 ~~~~~~~~r~~~~~~~  217 (302)
                      -|-|+=+-|-|.+-..
T Consensus       220 ~mkgriigreGrnir~  235 (520)
T PRK12704        220 EMKGRIIGREGRNIRA  235 (520)
T ss_pred             hhhcceeCCCcchHHH
Confidence            4455555666665444

>PRK00846 hypothetical protein; Provisional

Probab=83.60  E-value=17  Score=28.55  Aligned_cols=39  Identities=13%  Similarity=0.224  Sum_probs=21.9

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022126          144 SKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSA  182 (302)
Q Consensus       144 rKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa  182 (302)
                      ..-+++|.+...+--++..+|+.....|+.++..+..+.
T Consensus        26 e~tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~~~s~   64 (77)
T PRK00846         26 EQALTELSEALADARLTGARNAELIRHLLEDLGKVRSTL   64 (77)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            334444444455555556666666667777765555444

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

Probab=83.52  E-value=30  Score=33.54  Aligned_cols=18  Identities=11%  Similarity=0.054  Sum_probs=11.3

Q ss_pred             hcCCChHHHHHHHHHhhh
Q 022126           66 MAGVSPQILMKSAYRSVM   83 (302)
Q Consensus        66 L~GlsP~~Ime~a~RAi~   83 (302)
                      ..+.+|+...+++...+.
T Consensus       137 ~~~~dP~~A~~ian~l~~  154 (362)
T TIGR01010       137 VTAFDAEEAQKINQRLLK  154 (362)
T ss_pred             EEecCHHHHHHHHHHHHH
Confidence            447788876666555544

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

>PRK10920 putative uroporphyrinogen III C-methyltransferase; Provisional

Probab=83.52  E-value=21  Score=35.90  Aligned_cols=57  Identities=19%  Similarity=0.234  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 022126          102 AQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKS  158 (302)
Q Consensus       102 ~~lreK~e~L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKs  158 (302)
                      ..+.++.+.+.........++...++++..++..++.++..+.+..++|+.+|.+-+
T Consensus        70 ~~L~~ql~~~~~~~~~~~~~l~~~~~~~~~~l~~~e~~~~~l~~q~~~Lq~~~~~ls  126 (390)
T PRK10920         70 DALANQLTALQKAQESQKQELEGILKQQAKALDQANRQQAALAKQLDELQQKVATIS  126 (390)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344544445554444555556666666666677777777777777777777776633

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=83.34  E-value=40  Score=34.71  Aligned_cols=23  Identities=22%  Similarity=0.593  Sum_probs=15.3

Q ss_pred             EecCCccccHH----HHHhhhcCCCCC
Q 022126           16 STTCGHLLCTE----DANKILSNDAAC   38 (302)
Q Consensus        16 vT~CGHiFC~~----Ci~~~~~~~~~C   38 (302)
                      -..|||+-|-.    .+.++|+....|
T Consensus       243 cliCg~vgcgrY~eghA~rHweet~H~  269 (493)
T KOG0804|consen  243 CLICGNVGCGRYKEGHARRHWEETGHC  269 (493)
T ss_pred             EEEccceecccccchhHHHHHHhhcce
Confidence            45699999975    566677544333

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

Probab=83.34  E-value=34  Score=30.79  Aligned_cols=14  Identities=21%  Similarity=0.482  Sum_probs=7.6

Q ss_pred             CCChHHHHHHHHHh
Q 022126           68 GVSPQILMKSAYRS   81 (302)
Q Consensus        68 GlsP~~Ime~a~RA   81 (302)
                      -.+|+.+++.+-|-
T Consensus        21 ~EDP~~~l~q~ird   34 (221)
T PF04012_consen   21 AEDPEKMLEQAIRD   34 (221)
T ss_pred             hcCHHHHHHHHHHH
Confidence            34677666544443

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

>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=83.33  E-value=6.7  Score=30.74  Aligned_cols=54  Identities=20%  Similarity=0.323  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH---HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          121 QVHTAYQKMAKRCQMMEQEIES---LSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       121 e~~s~~~kl~~kl~~me~E~e~---LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      +++++...+++|++.+.+-++.   +.+..+|-.+.+++...+.++..++..++|.+
T Consensus        25 d~~~~~~~lk~Klq~ar~~i~~lpgi~~s~eeq~~~i~~Le~~i~~k~~~L~~~~~~   81 (83)
T PF07544_consen   25 DLDTATGSLKHKLQKARAAIRELPGIDRSVEEQEEEIEELEEQIRKKREVLQKFKER   81 (83)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4444445555555444443333   56666666666666666777777777777766

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. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex

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

Probab=83.31  E-value=21  Score=39.08  Aligned_cols=21  Identities=43%  Similarity=0.616  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHhHHHHHHHH
Q 022126          134 QMMEQEIESLSKDKQELQEKF  154 (302)
Q Consensus       134 ~~me~E~e~LrKkn~ELq~ky  154 (302)
                      .-|-.|.++|+..++|+|+++
T Consensus       482 e~~isei~qlqarikE~q~kl  502 (1118)
T KOG1029|consen  482 ELMISEIDQLQARIKELQEKL  502 (1118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            344456666666666666665

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=83.25  E-value=49  Score=36.18  Aligned_cols=15  Identities=7%  Similarity=-0.075  Sum_probs=8.0

Q ss_pred             CCChHHHHHHHHHhh
Q 022126           68 GVSPQILMKSAYRSV   82 (302)
Q Consensus        68 GlsP~~Ime~a~RAi   82 (302)
                      ..+|...++..-.+.
T Consensus       151 ~~~~~~~~~~~~~~~  165 (1179)
T TIGR02168       151 EAKPEERRAIFEEAA  165 (1179)
T ss_pred             cCCHHHHHHHHHHHc
Confidence            447776554444444

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.

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=83.23  E-value=0.52  Score=29.51  Aligned_cols=10  Identities=30%  Similarity=0.740  Sum_probs=6.0

Q ss_pred             ccccCccccc
Q 022126            2 RCNACWRELE   11 (302)
Q Consensus         2 ~CNiC~~~l~   11 (302)
                      .|+.|...+.
T Consensus         2 ~CP~C~~~V~   11 (26)
T PF10571_consen    2 TCPECGAEVP   11 (26)
T ss_pred             cCCCCcCCch
Confidence            3666666654

Several members are annotated as putative helicases.

>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=83.21  E-value=11  Score=36.48  Aligned_cols=66  Identities=14%  Similarity=0.287  Sum_probs=50.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          111 MQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       111 L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      .+.+|++--..+.=+++.|+.++.+|+..+-.++|++.|....++--.+.+..|+.-.+.||.++.
T Consensus        99 ~naQLDNek~~l~yqvd~Lkd~lee~eE~~~~~~re~~eK~~elEr~K~~~d~L~~e~~~Lre~L~  164 (302)
T PF09738_consen   99 SNAQLDNEKSALMYQVDLLKDKLEELEETLAQLQREYREKIRELERQKRAHDSLREELDELREQLK  164 (302)
T ss_pred             HHhhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356666666666667788888889999888888888888777776666677777777777887754

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.

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

Probab=83.21  E-value=17  Score=28.27  Aligned_cols=51  Identities=20%  Similarity=0.241  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022126          133 CQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSAI  183 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa~  183 (302)
                      +.+++..+.--.+-++||...+.|--.-..+++...+.|-.++..+..++.
T Consensus        10 i~eLE~r~AfQE~tieeLn~~laEq~~~i~k~q~qlr~L~~kl~~~~~~~~   60 (72)
T COG2900          10 IIELEIRLAFQEQTIEELNDALAEQQLVIDKLQAQLRLLTEKLKDLQPSAI   60 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc
Confidence            333333333334556677777776666666666655556555444444443

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=83.11  E-value=33  Score=36.25  Aligned_cols=35  Identities=11%  Similarity=0.265  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQE  152 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~  152 (302)
                      .+.+++..+.+++.++..++.+++.+++++.++.+
T Consensus       429 ~l~~l~~~l~~~~~~~~~~~~~~~~~~~~i~~~~~  463 (650)
T TIGR03185       429 ELGEAQNELFRSEAEIEELLRQLETLKEAIEALRK  463 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444444444444444444444444433

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.

>PF15254 CCDC14: Coiled-coil domain-containing protein 14

Probab=82.98  E-value=11  Score=40.92  Aligned_cols=56  Identities=14%  Similarity=0.314  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          114 KFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYD  169 (302)
Q Consensus       114 ~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYd  169 (302)
                      .|..++.+.-...+.|+.|.++|-+.+++++.+|..|.+.|.||..++.+....|+
T Consensus       438 ~Lq~ql~es~k~~e~lq~kneellk~~e~q~~Enk~~~~~~~ekd~~l~~~kq~~d  493 (861)
T PF15254_consen  438 SLQNQLQESLKSQELLQSKNEELLKVIENQKEENKRLRKMFQEKDQELLENKQQFD  493 (861)
T ss_pred             HHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            44455555556666777788888888888889999999999998887766555554

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=82.89  E-value=0.73  Score=49.98  Aligned_cols=40  Identities=25%  Similarity=0.546  Sum_probs=33.7

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQV   44 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~   44 (302)
                      .|..|.-.|.-..|-=.|||+|-..|+.   .+...||.|...
T Consensus       842 kCs~C~~~LdlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e  881 (933)
T KOG2114|consen  842 KCSACEGTLDLPFVHFLCGHSYHQHCLE---DKEDKCPKCLPE  881 (933)
T ss_pred             eecccCCccccceeeeecccHHHHHhhc---cCcccCCccchh
Confidence            5999999886556777899999999988   467899999873

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

Probab=82.82  E-value=43  Score=31.55  Aligned_cols=32  Identities=16%  Similarity=0.316  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 022126          123 HTAYQKMAKRCQMMEQEIESLSKDKQELQEKF  154 (302)
Q Consensus       123 ~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky  154 (302)
                      ...++.+..++..++...+.|.+.+.+|...|
T Consensus       222 r~~~~~l~~el~~l~~~~~~Le~~l~~le~~~  253 (312)
T PF00038_consen  222 RRQIQSLQAELESLRAKNASLERQLRELEQRL  253 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhhHhhhhhhccccchhhhhhhHHHHHHHH
Confidence            33333333333344444444444444443333

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 ....

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

Probab=82.80  E-value=20  Score=33.73  Aligned_cols=69  Identities=19%  Similarity=0.333  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          112 QEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSE--KSRQKRKLDEMYDQLRSEYESMKR  180 (302)
Q Consensus       112 ~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~E--KsRq~~qLqelYdkLK~~~e~~~r  180 (302)
                      .+.+.+.+..++.++..++.++..++.+++.++.+...+.+++..  ..|++..|+.-.+.++++..+++.
T Consensus        40 ~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e~kl~~v~~~~e~~aL~~E~~~ak~r~~~le~  110 (239)
T COG1579          40 LEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSLED  110 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455666667777777777777777777777777777777733  346777777777777777665554

>KOG4466 consensus Component of histone deacetylase complex (breast carcinoma metastasis suppressor 1 protein in human) [Cell cycle control, cell division, chromosome partitioning; Transcription]

Probab=82.68  E-value=20  Score=34.63  Aligned_cols=18  Identities=33%  Similarity=0.529  Sum_probs=9.3

Q ss_pred             ccCCCCCcccccccccCC
Q 022126          201 NMMDNRDPIRKDWSVYSP  218 (302)
Q Consensus       201 ~~~~~~~~~r~~~~~~~~  218 (302)
                      +|+++.-.|.+|-+.+.|
T Consensus       182 ~i~eD~~~i~k~~s~~~P  199 (291)
T KOG4466|consen  182 NILEDLRTINKDESAVQP  199 (291)
T ss_pred             hHHHHHhhhccccCCCCC
Confidence            455555555555555443

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=82.66  E-value=31  Score=29.79  Aligned_cols=23  Identities=30%  Similarity=0.592  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhc
Q 022126          161 KRKLDEMYDQLRSEYESMKRSAI  183 (302)
Q Consensus       161 ~~qLqelYdkLK~~~e~~~rsa~  183 (302)
                      +..+.--.|.+|.+|+++-.++.
T Consensus        97 ~s~~~~E~da~k~k~e~l~~~~~  119 (135)
T KOG4196|consen   97 NSRLRRELDAYKSKYEALQNSAV  119 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhh
Confidence            33334445567777777766655

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=82.65  E-value=0.23  Score=30.11  Aligned_cols=22  Identities=27%  Similarity=0.632  Sum_probs=10.9

Q ss_pred             cHHHHHhhhcCCCCCCCCcccc
Q 022126           24 CTEDANKILSNDAACPICDQVL   45 (302)
Q Consensus        24 C~~Ci~~~~~~~~~CPvC~~~l   45 (302)
                      |..|....-.....||.|+++|
T Consensus         2 Cp~CG~~~~~~~~fC~~CG~~l   23 (23)
T PF13240_consen    2 CPNCGAEIEDDAKFCPNCGTPL   23 (23)
T ss_pred             CcccCCCCCCcCcchhhhCCcC
Confidence            3444433333455566666643

>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]

Probab=82.60  E-value=41  Score=34.47  Aligned_cols=30  Identities=27%  Similarity=0.329  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 022126          134 QMMEQEIESLSKDKQELQEKFSEKSRQKRK  163 (302)
Q Consensus       134 ~~me~E~e~LrKkn~ELq~ky~EKsRq~~q  163 (302)
                      +.+++|++.||+...--|+.|.||--||++
T Consensus       256 ~~l~~EveRlrt~l~~Aqk~~~ek~~qy~~  285 (552)
T KOG2129|consen  256 DKLQAEVERLRTYLSRAQKSYQEKLMQYRA  285 (552)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346788888888888888888777766643

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

Probab=82.48  E-value=38  Score=30.69  Aligned_cols=100  Identities=15%  Similarity=0.257  Sum_probs=52.4

Q ss_pred             hcCCChHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Q 022126           66 MAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEK---LEQVHTAYQKMAKRCQMMEQEIES  142 (302)
Q Consensus        66 L~GlsP~~Ime~a~RAi~Fw~~Q~~qe~~yQ~~~l~~~lreK~e~L~~~l~~k---i~e~~s~~~kl~~kl~~me~E~e~  142 (302)
                      ..|++...+.....+-+.+-..|...--             ..+.+++++.++   ..+++..+.+++.++..++.+...
T Consensus        83 ~~GFnV~~l~~RL~kLL~lk~~~~~~~e-------------~~k~le~~~~~~~~~~~~~e~~i~~Le~ki~el~~~~~~  149 (190)
T PF05266_consen   83 EHGFNVKFLRSRLNKLLSLKDDQEKLLE-------------ERKKLEKKIEEKEAELKELESEIKELEMKILELQRQAAK  149 (190)
T ss_pred             HcCCccHHHHHHHHHHHHHHHhHHHHHH-------------HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            4577777776555555544444433211             001122222222   334555556666666666666566


Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          143 LSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       143 LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      ++.++++.......=.-...++.+-...++.++..+
T Consensus       150 ~~~~ke~~~~ei~~lks~~~~l~~~~~~~e~~F~~~  185 (190)
T PF05266_consen  150 LKEKKEAKDKEISRLKSEAEALKEEIENAELEFQSV  185 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            665555555444444445566666666777776655

>KOG4848 consensus Extracellular matrix-associated peroxidase [Extracellular structures; Defense mechanisms]

Probab=82.47  E-value=33  Score=31.57  Aligned_cols=61  Identities=25%  Similarity=0.273  Sum_probs=26.2

Q ss_pred             hcCCChHHHHHHHHHhhhhhhhhhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126           66 MAGVSPQILMKSAYRSVMFYLGQKELE-MQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKM  129 (302)
Q Consensus        66 L~GlsP~~Ime~a~RAi~Fw~~Q~~qe-~~yQ~~~l~~~lreK~e~L~~~l~~ki~e~~s~~~kl  129 (302)
                      -+|+.|.++...+..+-.|-+.|..+. ..-   +..+.++-++....++++....++..-+.++
T Consensus        83 ~SgV~p~~lfpS~e~~rE~~~~~~e~~e~l~---km~EslRi~~~~e~~k~~~Re~~iak~m~K~  144 (225)
T KOG4848|consen   83 KSGVPPEELFPSAEEIREFNNAKKEYKELLK---KMRESLRILYTKEPEKFTFREAEIAKNMKKY  144 (225)
T ss_pred             ccCCChhhhCCCHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence            455666655555554444444444321 100   1122333333334445555555544444443

>KOG4657 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.45  E-value=44  Score=31.45  Aligned_cols=44  Identities=14%  Similarity=0.154  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQK  161 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~  161 (302)
                      .+.+.+...-.+...+.+.+.++|.|++.+|-|.++|-++.+=+
T Consensus        80 L~~ek~~~q~~ieqeik~~q~elEvl~~n~Q~lkeE~dd~keiI  123 (246)
T KOG4657|consen   80 LKTEKEARQMGIEQEIKATQSELEVLRRNLQLLKEEKDDSKEII  123 (246)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Confidence            44444444445555677788899999999999998888665543

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=82.38  E-value=54  Score=32.40  Aligned_cols=40  Identities=15%  Similarity=0.297  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          135 MMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       135 ~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      .+..++..++.+..+|...|.++.-+...++.-.+.|+.+
T Consensus       258 ~l~~~l~~le~~l~~l~~~y~~~hP~v~~l~~~i~~l~~~  297 (444)
T TIGR03017       258 NLKTDIARAESKLAELSQRLGPNHPQYKRAQAEINSLKSQ  297 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHH
Confidence            4555556666666666666666555555544444444444

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.

>PRK11519 tyrosine kinase; Provisional

Probab=82.38  E-value=45  Score=35.73  Aligned_cols=31  Identities=16%  Similarity=0.255  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022126          152 EKFSEKSRQKRKLDEMYDQLRSEYESMKRSA  182 (302)
Q Consensus       152 ~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa  182 (302)
                      ..|.+-.|+..-.+++|+.|-.+++.++-+.
T Consensus       370 ~~~~~L~Re~~~~~~lY~~lL~r~~e~~i~~  400 (719)
T PRK11519        370 QEIVRLTRDVESGQQVYMQLLNKQQELKITE  400 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHh
Confidence            4455666777778889999888888776554

>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=82.24  E-value=42  Score=31.06  Aligned_cols=14  Identities=21%  Similarity=0.012  Sum_probs=9.8

Q ss_pred             CcccccccccCCCC
Q 022126          207 DPIRKDWSVYSPGT  220 (302)
Q Consensus       207 ~~~r~~~~~~~~~~  220 (302)
                      +.+|-|..++..-|
T Consensus       185 ~~LrlGr~~l~~~t  198 (251)
T PF11932_consen  185 DFLRLGRVALYYQT  198 (251)
T ss_pred             EEEeecchhheeEC
Confidence            45788888776555

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.

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=82.11  E-value=5.3  Score=32.75  Aligned_cols=22  Identities=9%  Similarity=0.191  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHH
Q 022126          130 AKRCQMMEQEIESLSKDKQELQ  151 (302)
Q Consensus       130 ~~kl~~me~E~e~LrKkn~ELq  151 (302)
                      +.+++.++++.+.|+.+++.|+
T Consensus        40 ~~e~~~l~~~n~~L~~eI~~L~   61 (105)
T PRK00888         40 QQTNAKLKARNDQLFAEIDDLK   61 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhh
Confidence            3334444445555555544444

>PRK01156 chromosome segregation protein; Provisional

Probab=81.93  E-value=63  Score=35.20  Aligned_cols=18  Identities=11%  Similarity=-0.136  Sum_probs=7.3

Q ss_pred             hHHHHHHHHHhhhhhhhh
Q 022126           71 PQILMKSAYRSVMFYLGQ   88 (302)
Q Consensus        71 P~~Ime~a~RAi~Fw~~Q   88 (302)
                      |+.-.+...+++.+..|+
T Consensus       148 ~~~r~~~ld~~~~~~~~~  165 (895)
T PRK01156        148 PAQRKKILDEILEINSLE  165 (895)
T ss_pred             HHHHHHHHHHHhChHHHH
Confidence            443333344444444443

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

Probab=81.82  E-value=64  Score=35.82  Aligned_cols=41  Identities=20%  Similarity=0.365  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          134 QMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       134 ~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      +++++..-..++++++|.++|.+--.++..|-.-|+....+
T Consensus       413 ee~e~~~l~~e~ry~klkek~t~l~~~h~~lL~K~~di~kQ  453 (980)
T KOG0980|consen  413 EEAENKALAAENRYEKLKEKYTELRQEHADLLRKYDDIQKQ  453 (980)
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333444444433333333333333333333

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

Probab=81.71  E-value=12  Score=35.26  Aligned_cols=13  Identities=23%  Similarity=0.271  Sum_probs=6.2

Q ss_pred             HHHHHHHHHHHHH
Q 022126          100 IVAQCRQKCEAMQ  112 (302)
Q Consensus       100 l~~~lreK~e~L~  112 (302)
                      ....+++|++.++
T Consensus       136 ~~ee~kekl~E~~  148 (290)
T COG4026         136 DYEELKEKLEELQ  148 (290)
T ss_pred             HHHHHHHHHHHHH
Confidence            3445555544443

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

Probab=81.67  E-value=21  Score=37.60  Aligned_cols=22  Identities=36%  Similarity=0.573  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHH
Q 022126          132 RCQMMEQEIESLSKDKQELQEK  153 (302)
Q Consensus       132 kl~~me~E~e~LrKkn~ELq~k  153 (302)
                      .+...+.|++.+++++.+|+..
T Consensus       302 Eie~kEeE~e~lq~~~d~Lk~~  323 (581)
T KOG0995|consen  302 EIEEKEEEIEKLQKENDELKKQ  323 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444433

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

Probab=81.63  E-value=79  Score=34.19  Aligned_cols=83  Identities=17%  Similarity=0.338  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCCCCCCC---
Q 022126          121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQ-------LRSEYESMKRSAIQPSNSFY---  190 (302)
Q Consensus       121 e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdk-------LK~~~e~~~rsa~~~a~~~~---  190 (302)
                      .+-+++..|+.|-..||..+....|-+.||=.+|-|-.||+.-++....+       ||.++.++++  +-|..++-   
T Consensus       591 ~L~~aL~amqdk~~~LE~sLsaEtriKldLfsaLg~akrq~ei~~~~~~~~d~ei~~lk~ki~~~~a--v~p~~~~~~~~  668 (697)
T PF09726_consen  591 VLMSALSAMQDKNQHLENSLSAETRIKLDLFSALGDAKRQLEIAQGQLRKKDKEIEELKAKIAQLLA--VMPSDSYCSAI  668 (697)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCccccccCC
Confidence            34455556666667777777777777778878888877777666655544       4555444433  34554433   


Q ss_pred             CCCCCCCcccccCCCC
Q 022126          191 PRNDPDLFSANMMDNR  206 (302)
Q Consensus       191 ~~~~~~~~~~~~~~~~  206 (302)
                      .-+.|+ ++..+|+..
T Consensus       669 ~~~~~~-~~~~~~~~~  683 (697)
T PF09726_consen  669 TPPTPH-YSSKFLNSS  683 (697)
T ss_pred             CCCCcc-chhhhccCC
Confidence            122333 445555543

; GO: 0016021 integral to membrane

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

Probab=81.62  E-value=36  Score=30.64  Aligned_cols=18  Identities=6%  Similarity=0.025  Sum_probs=11.8

Q ss_pred             HHHHHHhhhhhhhhhHHH
Q 022126           75 MKSAYRSVMFYLGQKELE   92 (302)
Q Consensus        75 me~a~RAi~Fw~~Q~~qe   92 (302)
                      .|-++-+.-||++=...-
T Consensus        47 ~EKiGssn~YWsFps~~~   64 (188)
T PF03962_consen   47 VEKIGSSNYYWSFPSQAK   64 (188)
T ss_pred             hhhccCeeEEEecChHHH
Confidence            355666777998865543

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

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

Probab=81.47  E-value=8.9  Score=28.57  Aligned_cols=22  Identities=23%  Similarity=0.409  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHH
Q 022126          129 MAKRCQMMEQEIESLSKDKQEL  150 (302)
Q Consensus       129 l~~kl~~me~E~e~LrKkn~EL  150 (302)
                      ++.+++.++.+.+.|+++++.|
T Consensus        29 l~~~i~~l~~e~~~L~~ei~~l   50 (80)
T PF04977_consen   29 LQKEIEELKKENEELKEEIERL   50 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHh
Confidence            3333334444444444444443

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

>KOG4571 consensus Activating transcription factor 4 [Transcription]

Probab=81.26  E-value=13  Score=36.01  Aligned_cols=40  Identities=28%  Similarity=0.395  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          132 RCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQL  171 (302)
Q Consensus       132 kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkL  171 (302)
                      +.+++..|++.|.++|+||++...+-.|+++-|..++-..
T Consensus       249 e~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~  288 (294)
T KOG4571|consen  249 EKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEV  288 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467788888999999999988888888888887666544

>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=81.18  E-value=40  Score=36.86  Aligned_cols=61  Identities=16%  Similarity=0.329  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          114 KFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       114 ~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      .+..++...++.+.+....+..++.|...+.-++.+|.+.|.-+.+++..|+.-|+.|...
T Consensus       347 ~Lr~rle~k~~~l~kk~~~~~~~qeE~~~~~~Ei~~l~d~~d~~e~ki~~Lq~kie~Lee~  407 (775)
T PF10174_consen  347 ALRFRLEEKNSQLEKKQAQIEKLQEEKSRLQGEIEDLRDMLDKKERKINVLQKKIENLEEQ  407 (775)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456777788888888888899999999999999999999999999998888777665433

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 [].

>KOG1850 consensus Myosin-like coiled-coil protein [Cytoskeleton]

Probab=81.14  E-value=43  Score=33.18  Aligned_cols=34  Identities=26%  Similarity=0.349  Sum_probs=21.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          138 QEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQL  171 (302)
Q Consensus       138 ~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkL  171 (302)
                      .+.+.|+..|-||.+++.+-..||....+.||++
T Consensus       130 ~~n~klre~NieL~eKlkeL~eQy~~re~hidk~  163 (391)
T KOG1850|consen  130 SKNDKLREDNIELSEKLKELGEQYEEREKHIDKQ  163 (391)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3556666666666666666666666666566554

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

Probab=81.05  E-value=6.9  Score=27.50  Aligned_cols=34  Identities=18%  Similarity=0.424  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 022126          122 VHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFS  155 (302)
Q Consensus       122 ~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~  155 (302)
                      ++..|+-|+.....+..+.+.|.++|++|+....
T Consensus         3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~   36 (45)
T PF02183_consen    3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQ   36 (45)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445666666666666666666666666654443

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

>PF10212 TTKRSYEDQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019348 This entry represents a C-terminal 500 residue region, which contains a conserved TTKRSYEDQ motif

Probab=81.04  E-value=24  Score=36.70  Aligned_cols=65  Identities=18%  Similarity=0.378  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          112 QEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDK-------QELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       112 ~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn-------~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      ...|..+|.++-.+++.+..|...+..|++.|.++.       +-+.+.+++...++..||+-....|+.||
T Consensus       415 k~~Y~~RI~eLt~qlQ~adSKa~~f~~Ec~aL~~rL~~aE~ek~~l~eeL~~a~~~i~~LqDEL~TTr~NYE  486 (518)
T PF10212_consen  415 KSYYMSRIEELTSQLQHADSKAVHFYAECRALQKRLESAEKEKESLEEELKEANQNISRLQDELETTRRNYE  486 (518)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence            334444444444444444434333333333333322       23334444444444455544444444444

It is found in a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. These proteins also contain an N-terminal domain with a KLRAQ motif (IPR019343 from INTERPRO). The function of these proteins is not known.

>KOG0709 consensus CREB/ATF family transcription factor [Transcription]

Probab=81.03  E-value=30  Score=35.61  Aligned_cols=45  Identities=20%  Similarity=0.218  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 022126          123 HTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEM  167 (302)
Q Consensus       123 ~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqel  167 (302)
                      +..++.|+.++..-.+|...|+||++||...=+.=--|++|||.+
T Consensus       271 keYid~LE~rv~~~taeNqeL~kkV~~Le~~N~sLl~qL~klQt~  315 (472)
T KOG0709|consen  271 KEYIDGLESRVSAFTAENQELQKKVEELELSNRSLLAQLKKLQTL  315 (472)
T ss_pred             hhHHHHHhhhhhhcccCcHHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence            334555666665555555555555555533322222344444433

>PRK09039 hypothetical protein; Validated

Probab=80.99  E-value=33  Score=33.68  Aligned_cols=55  Identities=5%  Similarity=0.077  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLR  172 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK  172 (302)
                      .+.+.+.++..|+.++..++.++..++-.+.++.+..+|...++..|+...+...
T Consensus       131 ~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~  185 (343)
T PRK09039        131 VSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVAL  185 (343)
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555666666666666666666666666666666666666666655555553

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

Probab=80.93  E-value=34  Score=36.01  Aligned_cols=112  Identities=18%  Similarity=0.212  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH-HHHHhhcCCCC
Q 022126          113 EKFTEKLEQVHTAYQKMAKRCQ---MMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMY-DQLRSEYE-SMKRSAIQPSN  187 (302)
Q Consensus       113 ~~l~~ki~e~~s~~~kl~~kl~---~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelY-dkLK~~~e-~~~rsa~~~a~  187 (302)
                      ++|.-.+.++=...++++.+++   ..+..++.|+++..+|..+|.+.++++.+...-| ..|...+. .++.-++.-|.
T Consensus       314 RKY~~~~~~l~~~~~~~~~el~~L~~~~~~~~~Le~~~~~l~~~~~~~A~~Ls~~R~~~A~~L~~~v~~eL~~L~Me~a~  393 (557)
T COG0497         314 RKYGVTIEDLLEYLDKIKEELAQLDNSEESLEALEKEVKKLKAELLEAAEALSAIRKKAAKELEKEVTAELKALAMEKAR  393 (557)
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCce
Confidence            3333333333333444444433   4456678889999999999988888876665544 33444433 35554553332


Q ss_pred             CCCCCCCCCCcccccCCCCCcccccccccCCCCCCCCCC
Q 022126          188 SFYPRNDPDLFSANMMDNRDPIRKDWSVYSPGTPGPRED  226 (302)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~  226 (302)
                       |.-.=.|.-+.|+ -+|-|.|-+..+++.|..|+|=..
T Consensus       394 -F~ve~~~~~~~~t-~~G~d~VeF~istNpG~~~~PL~K  430 (557)
T COG0497         394 -FTVELKPLEESPT-ADGADKVEFLISTNPGEPLKPLAK  430 (557)
T ss_pred             -EEEEeccCCCCCC-cCCcceEEEEEeCCCCCCCccHHh
Confidence             2111111111122 278888999988884444666443

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

Probab=80.54  E-value=40  Score=31.08  Aligned_cols=36  Identities=25%  Similarity=0.401  Sum_probs=14.9

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          139 EIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       139 E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      .+..|..++.+.-..+..-.|...+|+.-.+.|...
T Consensus       177 ~i~~L~~~lkeaE~Rae~aE~~v~~Le~~id~le~e  212 (237)
T PF00261_consen  177 KIRDLEEKLKEAENRAEFAERRVKKLEKEIDRLEDE  212 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333344444444444444444433

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 ....

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

Probab=80.47  E-value=49  Score=32.72  Aligned_cols=28  Identities=21%  Similarity=0.241  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          151 QEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       151 q~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      ...|.||..|++.|+.+.+.++..-...
T Consensus       186 ~~vLNeKK~KIR~lq~~L~~~~~~~~~~  213 (342)
T PF06632_consen  186 VLVLNEKKAKIRELQRLLASAKEEEKSP  213 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhHHHHHHHHHHHHHHhhccccch
Confidence            3447899999999999999988754433

XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.

>PRK03918 chromosome segregation protein; Provisional

Probab=80.40  E-value=51  Score=35.55  Aligned_cols=14  Identities=29%  Similarity=0.973  Sum_probs=11.5

Q ss_pred             CCCCCCCccccccC
Q 022126           35 DAACPICDQVLSKS   48 (302)
Q Consensus        35 ~~~CPvC~~~l~~~   48 (302)
                      ...||+|+.+|...
T Consensus       435 ~~~Cp~c~~~L~~~  448 (880)
T PRK03918        435 KGKCPVCGRELTEE  448 (880)
T ss_pred             CCCCCCCCCcCCch
Confidence            46899999999764

>PF12240 Angiomotin_C: Angiomotin C terminal; InterPro: IPR024646 This domain represents the C-terminal region of angiomotin

Probab=80.33  E-value=21  Score=32.90  Aligned_cols=41  Identities=22%  Similarity=0.323  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--H-HHHhhcCCCC
Q 022126          147 KQELQEKFSEKSRQKRKLDEMYDQLRSEYE--S-MKRSAIQPSN  187 (302)
Q Consensus       147 n~ELq~ky~EKsRq~~qLqelYdkLK~~~e--~-~~rsa~~~a~  187 (302)
                      ...|++.++||.-++..|+.-.-+...+|-  . +|-.|+++|+
T Consensus        59 ~~~L~~~LrEkEErILaLEad~~kWEqkYLEEs~mrq~a~dAaa  102 (205)
T PF12240_consen   59 ASNLKELLREKEERILALEADMTKWEQKYLEESAMRQFAMDAAA  102 (205)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            567999999999999999999999988873  3 3445555443

Angiomotin regulates the action of angiogenesis-inhibitor angiostatin []. The C-terminal region of angiomotin appears to be involved in directing the protein chemotactically [].

>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]

Probab=80.21  E-value=49  Score=35.02  Aligned_cols=47  Identities=4%  Similarity=0.058  Sum_probs=24.2

Q ss_pred             hcCCChHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126           66 MAGVSPQILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFT  116 (302)
Q Consensus        66 L~GlsP~~Ime~a~RAi~Fw~~Q~~qe~~yQ~~~l~~~lreK~e~L~~~l~  116 (302)
                      ++..+|.+-.++..+++..+-.   +++.|+. .+-..++.....++.+.+
T Consensus       552 ~SsP~~~E~~~lL~~a~~vfrE---qYi~~~d-lV~~e~qrH~~~l~~~k~  598 (741)
T KOG4460|consen  552 SSAPPPEECLQLLSRATQVFRE---QYILKQD-LVKEEIQRHVKLLCDQKK  598 (741)
T ss_pred             ccCCCcHHHHHHHHHHHHHHHH---HHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence            3445566667777788765443   3455553 333344444344443333

>cd07656 F-BAR_srGAP The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Proteins

Probab=80.17  E-value=48  Score=30.98  Aligned_cols=52  Identities=19%  Similarity=0.330  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHH
Q 022126          125 AYQKMAKRCQMMEQEIESLSKDKQELQEKFS----------EKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       125 ~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~----------EKsRq~~qLqelYdkLK~~~e  176 (302)
                      ++++.++......++-+.-+++..+......          ++.++..+++...++.+.++.
T Consensus       132 eL~k~kK~Y~~~~~ea~~A~~K~~~ae~~~~k~~~~~~~~~~~~~~~~~~~~~~eK~k~k~~  193 (241)
T cd07656         132 ELQTAMKTYHTYHAESKSAERKLKEAEKQEEKQEQSPEKKLERSRSSKKIEKEVEKRQAKYS  193 (241)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444455555555555555544443          233444456666666666654

F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs, all of which are expressed during embryonic and early development in the nervous system but with different localization and timing. srGAPs contain an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.

>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=80.13  E-value=14  Score=32.19  Aligned_cols=40  Identities=35%  Similarity=0.620  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHH--------HHHHHHHHHHHHHHHHHH
Q 022126          135 MMEQEIESLSKDKQELQEKFSE--------KSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       135 ~me~E~e~LrKkn~ELq~ky~E--------KsRq~~qLqelYdkLK~~  174 (302)
                      +|..+++.|+.++.+|..++..        -..+..++...|.+++..
T Consensus       113 el~~~i~~l~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~k~  160 (169)
T PF07106_consen  113 ELREEIEELEEEIEELEEKLEKLRSGSKPVSPEEKEKLEKEYKKWRKE  160 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHH
Confidence            4444455555555555554442        123445566666555544

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 [].

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=80.10  E-value=14  Score=39.14  Aligned_cols=42  Identities=10%  Similarity=0.249  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSR  159 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsR  159 (302)
                      |-++++++|.++..|++++++++.+-+.+..-|+...+...+
T Consensus       101 krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~  142 (907)
T KOG2264|consen  101 KRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQR  142 (907)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHH
Confidence            556677777777777777776666555555555444444333

>KOG0289 consensus mRNA splicing factor [General function prediction only]

Probab=80.06  E-value=15  Score=37.68  Aligned_cols=54  Identities=19%  Similarity=0.273  Sum_probs=44.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVD   54 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~~   54 (302)
                      |.|.|-.+......|...-||+|=+.-|.++......||+-+.+|+..++|++.
T Consensus         1 m~CaISgEvP~~PVvS~~Sg~vfEkrLIEqyI~e~G~DPIt~~pLs~eelV~Ik   54 (506)
T KOG0289|consen    1 MVCAISGEVPEEPVVSPVSGHVFEKRLIEQYIAETGKDPITNEPLSIEELVEIK   54 (506)
T ss_pred             CeecccCCCCCCccccccccchHHHHHHHHHHHHcCCCCCCCCcCCHHHeeecc
Confidence            678888876654344455899999999999999999999999999998887764

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

Probab=80.06  E-value=83  Score=35.72  Aligned_cols=27  Identities=33%  Similarity=0.491  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 022126          131 KRCQMMEQEIESLSKDKQELQEKFSEK  157 (302)
Q Consensus       131 ~kl~~me~E~e~LrKkn~ELq~ky~EK  157 (302)
                      .++...+.+++.++.+.+|+.+.+...
T Consensus       260 ~~~~~~~~~i~~~~~~~~e~~~~~~~~  286 (1163)
T COG1196         260 EELEEAEKEIEELKSELEELREELEEL  286 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333444444444444444444443

---

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	302
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-04
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	4e-04
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	7e-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 = 56.4 bits (135), Expect = 5e-09
 Identities = 34/238 (14%), Positives = 74/238 (31%), Gaps = 55/238 (23%)

Query: 43  QVLSKSLMKPVDINPNDE-------WVNMAMAGVSPQILMKSAYRSVMFYLGQKELEMQY 95
            +LSK  +  + ++ +         W            L+      V  ++ +  L + Y
Sbjct: 44  SILSKEEIDHIIMSKDAVSGTLRLFW-----------TLLSKQEEMVQKFVEEV-LRINY 91

Query: 96  K--MNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQ-E 152
           K  M+ I  + RQ    M   + E+ ++++   Q  AK      Q    L +   EL+  
Sbjct: 92  KFLMSPIKTEQRQP-SMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPA 150

Query: 153 KF--------SEKS-------RQKRKLDEMYDQ---LRSEYESMKRSAIQPSNSFYPRND 194
           K         S K+          +   +M  +   L  +  +   + ++       + D
Sbjct: 151 KNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQID 210

Query: 195 PDLFSANMMDNRDPIRKDW-----SVYSPGTPGPR-----EDIWPARQNSSNSGPFDI 242
           P+  S +   +   +R               P         ++     N+     F++
Sbjct: 211 PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ----NAKAWNAFNL 264

>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 = 49.9 bits (118), Expect = 7e-07
 Identities = 23/152 (15%), Positives = 53/152 (34%), Gaps = 33/152 (21%)

Query: 92  EMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQ 151
           E QY+   I+          ++ F +  +            C+ ++   +S+   K+E+ 
Sbjct: 13  EHQYQYKDIL-------SVFEDAFVDNFD------------CKDVQDMPKSILS-KEEID 52

Query: 152 EKFSEKSRQKRKLDEMYDQLRSEYESM-KR---SAIQPSNSF------YPRNDPDLFSAN 201
                K         ++  L S+ E M ++     ++ +  F        +  P + +  
Sbjct: 53  HIIMSKDAVSG-TLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRM 111

Query: 202 MMDNRDPIRKDWSVYSPGTPGPR-EDIWPARQ 232
            ++ RD +  D  V++      R +     RQ
Sbjct: 112 YIEQRDRLYNDNQVFAKYNV-SRLQPYLKLRQ 142

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 47.5 bits (113), Expect = 3e-06
 Identities = 13/90 (14%), Positives = 38/90 (42%), Gaps = 1/90 (1%)

Query: 92  EMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQ 151
           E +    R+ A+ ++  E +  +   ++E+     Q++    + M+Q++  L +  +E +
Sbjct: 910 EAEEMRVRLAAKKQEL-EEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEE 968

Query: 152 EKFSEKSRQKRKLDEMYDQLRSEYESMKRS 181
               +   +K   D    ++  +   M+  
Sbjct: 969 AARQKLQLEKVTADGKIKKMEDDILIMEDQ 998

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 44.8 bits (106), Expect = 2e-05
 Identities = 18/97 (18%), Positives = 39/97 (40%)

Query: 88   QKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDK 147
               L  + +  + + + + K E+M  +   +L++   + Q++ K  + +E E   L +  
Sbjct: 1017 TTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQI 1076

Query: 148  QELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSAIQ 184
             ELQ + +E   Q  K +E      +  E        
Sbjct: 1077 AELQAQIAELKAQLAKKEEELQAALARLEDETSQKNN 1113

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 43.7 bits (103), Expect = 6e-05
 Identities = 13/93 (13%), Positives = 44/93 (47%)

Query: 88   QKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDK 147
            +  +E + + ++ +   ++K +       E+LE+   A QK+       + +I+ +  D 
Sbjct: 933  EARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDI 992

Query: 148  QELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
              ++++ ++ +++++ L+E    L +     + 
Sbjct: 993  LIMEDQNNKLTKERKLLEERVSDLTTNLAEEEE 1025

>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 = 42.1 bits (99), Expect = 2e-04
 Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 1/92 (1%)

Query: 86   LGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSK 145
            L ++  E+Q ++  + AQ  +K E   +    +LE   +      K+ + +E  I  L +
Sbjct: 1072 LHEQIAELQAQIAELKAQLAKK-EEELQAALARLEDETSQKNNALKKIRELESHISDLQE 1130

Query: 146  DKQELQEKFSEKSRQKRKLDEMYDQLRSEYES 177
            D +  +   ++  +QKR L E  + L++E E 
Sbjct: 1131 DLESEKAARNKAEKQKRDLSEELEALKTELED 1162

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

 Score = 45.1 bits (107), Expect = 2e-05
 Identities = 12/109 (11%), Positives = 43/109 (39%)

Query: 73  ILMKSAYRSVMFYLGQKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKR 132
           + ++  YR +M     K+L+++ +      +     E    +   K+++ +  Y+ + ++
Sbjct: 891 VYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEK 950

Query: 133 CQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRS 181
              +E    + ++  +   E+      + +        L+ E   +++ 
Sbjct: 951 MNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKE 999

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

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 13/93 (13%), Positives = 42/93 (45%), Gaps = 3/93 (3%)

Query: 88   QKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDK 147
              + E+  K+ + + Q + + + ++E   +   +      ++ ++  +++ E E L++  
Sbjct: 988  SLQEEIA-KLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRI 1046

Query: 148  QELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR 180
             +  ++ +E    ++KL E   QL  +    + 
Sbjct: 1047 HDQAKEITE--TMEKKLVEETKQLELDLNDERL 1077

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

 Score = 40.9 bits (96), Expect = 4e-04
 Identities = 16/111 (14%), Positives = 46/111 (41%), Gaps = 17/111 (15%)

Query: 88   QKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQV----------HTAYQKMAKRCQMME 137
            ++  ++   +   + Q ++K +   +++   LE++              +   +R +M E
Sbjct: 917  ERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSE 976

Query: 138  QEIESLSKDKQELQEK-------FSEKSRQKRKLDEMYDQLRSEYESMKRS 181
            +E ++ +     LQE+         +   +K+ ++E  D+ + E E +   
Sbjct: 977  EEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSE 1027

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

 Score = 40.5 bits (95), Expect = 6e-04
 Identities = 13/91 (14%), Positives = 33/91 (36%), Gaps = 1/91 (1%)

Query: 88  QKELEMQYKMNRIVAQCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDK 147
            +    +     +  QC  +   M ++  +KL+    + ++  K    +E +I  L +  
Sbjct: 879 ARVHYHRTLKAIVYLQCCYR-RMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKI 937

Query: 148 QELQEKFSEKSRQKRKLDEMYDQLRSEYESM 178
            E  +++     +   L+  Y     +  S 
Sbjct: 938 DEQNKEYKSLLEKMNNLEITYSTETEKLRSD 968

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B* Length = 63

 Score = 37.1 bits (86), Expect = 4e-04
 Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 2/41 (4%)

Query: 3  CNACW-RELEGRAISTTCGHL-LCTEDANKILSNDAACPIC 41
          C+ C  R  +G  I    GHL  C   A ++    A+CPIC
Sbjct: 10 CSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPIC 50

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 36.7 bits (85), Expect = 7e-04
 Identities = 13/54 (24%), Positives = 19/54 (35%), Gaps = 1/54 (1%)

Query: 2  RCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDI 55
          RC  C +  +   + T C H  C   A +       C ICDQ          ++
Sbjct: 17 RCFICRQAFQ-NPVVTKCRHYFCESCALEHFRATPRCYICDQPTGGIFNPAKEL 69

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	302
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.22
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.17
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.17
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.17
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.16
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.16
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.14
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.14
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.13
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.12
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.11
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.1
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.1
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.09
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.08
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.08
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.06
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.06
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.05
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.04
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.03
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.02
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.02
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.02
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.01
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.0
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.99
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	98.99
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	98.98
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.98
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	98.95
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.95
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.95
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.94
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	98.93
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.92
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.91
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.91
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	98.9
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.9
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.89
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	98.86
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.85
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.84
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.84
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.81
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	98.8
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.78
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.77
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.76
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.74
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.72
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.69
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.62
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.53
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.49
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.48
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.47
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.35
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.34
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.22
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.19
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.85
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	97.77
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	97.55
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.74
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	96.11
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	95.72
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	95.1
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	94.95
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	94.77
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	94.72
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.66
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	94.46
3mq9_A	471	Bone marrow stromal antigen 2 fused to maltose-BI	94.32
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	94.13
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	93.77
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	93.71
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	93.0
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	92.66
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	92.5
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	92.35
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	91.94
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	91.86
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	91.72
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	91.64
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	91.62
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	91.57
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	91.41
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	91.35
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	91.24
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	91.08
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	90.25
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	90.2
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	90.12
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	89.97
3t98_B	93	Nucleoporin NUP58/NUP45; NUP62 complex, nuclear im	89.87
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	89.85
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	89.77
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	89.7
3iox_A	497	AGI/II, PA; alpha helix, PPII helix, supersandwich	89.51
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	89.5
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	89.43
2wt7_B	90	Transcription factor MAFB; transcription, transcri	88.9
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	88.86
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	88.56
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	88.23
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	88.15
3swk_A	86	Vimentin; cytoskeleton, intermediate filament, alp	87.8
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	87.71
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	87.25
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	86.6
1x79_B	112	RAB GTPase binding effector protein 1; rabaptin5,	85.97
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	85.17
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	84.87
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	84.33
3q0x_A	228	Centriole protein; centrosome protein, coiled coil	84.28
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	84.25
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	84.19
3vmx_A	48	Voltage-gated hydrogen channel 1; coiled-coil, ION	83.68
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	83.03
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	82.88
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	82.82
3htk_A	60	Structural maintenance of chromosomes protein 5; S	82.68
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	82.43
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	82.24
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	82.24
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	82.15
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	81.9
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	81.62
2efr_A	155	General control protein GCN4 and tropomyosin 1 Al;	81.53
3l4q_C	170	Phosphatidylinositol 3-kinase regulatory subunit b	81.44
1p9i_A	31	Cortexillin I/GCN4 hybrid peptide; coiled-coil, un	81.3
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	81.18
3cl3_D	130	NF-kappa-B essential modulator; death effector dom	81.15
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	81.02
1deb_A	54	APC protein, adenomatous polyposis coli protein; c	80.98
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	80.85
4dzo_A	123	Mitotic spindle assembly checkpoint protein MAD1;	80.38
2oto_A	155	M protein; helical coiled coil, fibrinogen-binding	80.37
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	80.24
2efr_A	155	General control protein GCN4 and tropomyosin 1 Al;	80.18
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	80.13

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=99.22  E-value=6.8e-12  Score=94.06  Aligned_cols=51  Identities=18%  Similarity=0.386  Sum_probs=44.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~div~   52 (302)
                      +.|+||...+. +||++.|||+||..|+.+|+.. ...||+|++.+...++++
T Consensus         9 ~~C~IC~~~~~-~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~   60 (78)
T 1t1h_A            9 FRCPISLELMK-DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTP   60 (78)
T ss_dssp             SSCTTTSCCCS-SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEE
T ss_pred             CCCCCcccccc-CCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCcc
Confidence            57999999886 6999999999999999999986 789999999998665543

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=99.17  E-value=1.1e-11  Score=95.84  Aligned_cols=51  Identities=18%  Similarity=0.230  Sum_probs=45.5

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~   52 (302)
                      |.|+||...+. +||++.|||+||..||.+|+....+||+|+..++..++++
T Consensus        15 ~~CpI~~~~m~-dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~p   65 (85)
T 2kr4_A           15 FRDPLMDTLMT-DPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESMLEP   65 (85)
T ss_dssp             TBCTTTCSBCS-SEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCEE
T ss_pred             eECcccCchhc-CCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHhcch
Confidence            68999999986 6999999999999999999988889999999998665544

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=1.3e-11  Score=91.60  Aligned_cols=51  Identities=22%  Similarity=0.455  Sum_probs=44.1

Q ss_pred             CccccCcccccCCcEEe-cCCccccHHHHHhhhcCCCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAIST-TCGHLLCTEDANKILSNDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT-~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~   52 (302)
                      +.|+||...+.+ ++++ .|||+||..|+.+|+.....||+|++.+...+++.
T Consensus        16 ~~C~IC~~~~~~-p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   67 (72)
T 2djb_A           16 ILCSICKGYLID-ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLS   67 (72)
T ss_dssp             GSCTTTSSCCSS-CEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCC
T ss_pred             CCCCCCChHHHC-cCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCcccccc
Confidence            469999999864 6664 99999999999999988899999999998776644

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=99.17  E-value=1.6e-11  Score=98.05  Aligned_cols=51  Identities=18%  Similarity=0.227  Sum_probs=45.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~   52 (302)
                      |.|+||...+. +||++.|||+||..||.+||....+||+|+.+++..++++
T Consensus        30 ~~CpI~~~~m~-dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~p   80 (100)
T 2kre_A           30 FRDPLMDTLMT-DPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEP   80 (100)
T ss_dssp             TBCTTTCSBCS-SEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEE
T ss_pred             hCCcCccCccc-CCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhceE
Confidence            68999999986 6999999999999999999988889999999998765544

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.16  E-value=1.3e-11  Score=90.04  Aligned_cols=49  Identities=27%  Similarity=0.632  Sum_probs=42.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc-CCCCCCCCccccccCCC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS-NDAACPICDQVLSKSLM   50 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~-~~~~CPvC~~~l~~~di   50 (302)
                      +.|+||...+. +++++.|||+||..|+.+|+. ....||+|++.+...++
T Consensus        16 ~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~i   65 (66)
T 2ecy_A           16 YKCEKCHLVLC-SPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKV   65 (66)
T ss_dssp             EECTTTCCEES-SCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTTC
T ss_pred             CCCCCCChHhc-CeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhhc
Confidence            36999999986 588899999999999999995 57789999999887665

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=99.16  E-value=1.5e-11  Score=90.15  Aligned_cols=53  Identities=26%  Similarity=0.708  Sum_probs=45.6

Q ss_pred             CccccCcccccC------CcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCccc
Q 022126            1 MRCNACWRELEG------RAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPV   53 (302)
Q Consensus         1 l~CNiC~~~l~~------~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~   53 (302)
                      +.|+||+..+.+      .++++.|||+||..|+.+|+.....||+|++.+...++.++
T Consensus        11 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   69 (71)
T 3ng2_A           11 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI   69 (71)
T ss_dssp             CBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCCCC
T ss_pred             CCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhheeec
Confidence            469999998853      12899999999999999999888999999999988777654

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=99.14  E-value=1.6e-11  Score=87.95  Aligned_cols=53  Identities=26%  Similarity=0.708  Sum_probs=45.7

Q ss_pred             CccccCcccccC------CcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCccc
Q 022126            1 MRCNACWRELEG------RAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPV   53 (302)
Q Consensus         1 l~CNiC~~~l~~------~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~   53 (302)
                      +.|+||+..+.+      .++++.|||+||..|+.+|+.....||.|++.+...++.++
T Consensus         4 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   62 (64)
T 2xeu_A            4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI   62 (64)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCEEEC
T ss_pred             CCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccceeee
Confidence            469999998853      23899999999999999999888999999999988777654

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}

Probab=99.14  E-value=2e-11  Score=96.53  Aligned_cols=51  Identities=27%  Similarity=0.552  Sum_probs=44.8

Q ss_pred             CccccCcccccCCcEE-ecCCccccHHHHHhhhcCC-CCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAIS-TTCGHLLCTEDANKILSND-AACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vv-T~CGHiFC~~Ci~~~~~~~-~~CPvC~~~l~~~div~   52 (302)
                      +.|+||...+. .|++ +.|||+||..||.+|+... ..||+|++.+...+++.
T Consensus        23 ~~C~IC~~~~~-~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l~~   75 (100)
T 3lrq_A           23 FRCFICMEKLR-DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVN   75 (100)
T ss_dssp             TBCTTTCSBCS-SEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEE
T ss_pred             CCCccCCcccc-CccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHhHh
Confidence            57999999996 5888 9999999999999999876 79999999998766654

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=99.13  E-value=2.7e-11  Score=100.90  Aligned_cols=46  Identities=24%  Similarity=0.654  Sum_probs=41.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      +.|+||...+. +||++.|||+||..|+..|+.....||+|++.+..
T Consensus        54 ~~C~iC~~~~~-~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           54 LQCIICSEYFI-EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             SBCTTTCSBCS-SEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             CCCcccCcccC-CceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            46999999986 69999999999999999999989999999998754

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.12  E-value=4e-11  Score=88.45  Aligned_cols=49  Identities=24%  Similarity=0.646  Sum_probs=42.6

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc---CCCCCCCCccccccCCC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS---NDAACPICDQVLSKSLM   50 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~---~~~~CPvC~~~l~~~di   50 (302)
                      +.|+||+..+. +++++.|||+||..|+.+|+.   ....||+|++.+...++
T Consensus        21 ~~C~IC~~~~~-~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           21 VICPICLDILQ-KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAI   72 (73)
T ss_dssp             CBCTTTCSBCS-SEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCCC
T ss_pred             CEeccCCcccC-CeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcccC
Confidence            47999999886 699999999999999999986   46789999999876554

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=99.11  E-value=4.3e-11  Score=95.20  Aligned_cols=51  Identities=10%  Similarity=0.058  Sum_probs=45.7

Q ss_pred             CccccCcccccCCcEEecCC-ccccHHHHHhhhcCCCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCG-HLLCTEDANKILSNDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CG-HiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~   52 (302)
                      |.|+||...+. +||++.|| |+||..||.+||....+||+|+.++...++++
T Consensus        23 ~~CpI~~~~m~-dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~p   74 (98)
T 1wgm_A           23 FLDPIMSTLMC-DPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRP   74 (98)
T ss_dssp             TBCTTTCSBCS-SEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEE
T ss_pred             cCCcCcccccc-CCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceE
Confidence            68999999986 69999999 99999999999988889999999998765544

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.10  E-value=3.4e-11  Score=89.07  Aligned_cols=49  Identities=18%  Similarity=0.491  Sum_probs=43.5

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLM   50 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~di   50 (302)
                      +.|+||+..+. +++++.|||+||..|+.+|+.....||+|+..+...++
T Consensus        16 ~~C~IC~~~~~-~~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~   64 (71)
T 2d8t_A           16 PECAICLQTCV-HPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFL   64 (71)
T ss_dssp             CBCSSSSSBCS-SEEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHHHH
T ss_pred             CCCccCCcccC-CCEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHhhc
Confidence            46999999885 68999999999999999998888999999999876554

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.10  E-value=4.9e-11  Score=89.61  Aligned_cols=51  Identities=24%  Similarity=0.602  Sum_probs=44.1

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC------CCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN------DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~------~~~CPvC~~~l~~~div~   52 (302)
                      +.|+||+..+. .++++.|||+||..|+..|+..      ...||.|++.+...++.+
T Consensus        20 ~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~   76 (85)
T 2ecw_A           20 VTCPICLELLK-EPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKP   76 (85)
T ss_dssp             TSCTTTCSCCS-SCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCEE
T ss_pred             CCCcCCChhhC-cceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCCc
Confidence            47999999986 5889999999999999999875      678999999998766543

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.09  E-value=4.5e-11  Score=90.46  Aligned_cols=45  Identities=29%  Similarity=0.663  Sum_probs=41.4

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      +.|+||+..+. .++++.|||+||..|+.+|+.....||+|++.+.
T Consensus        16 ~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           16 FRCFICRQAFQ-NPVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             SBCSSSCSBCC-SEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCcCCCchhc-CeeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            47999999986 5999999999999999999988899999999886

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=99.08  E-value=3.1e-11  Score=90.19  Aligned_cols=50  Identities=26%  Similarity=0.609  Sum_probs=43.2

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-------CCCCCCCccccccCCCc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-------DAACPICDQVLSKSLMK   51 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-------~~~CPvC~~~l~~~div   51 (302)
                      +.|+||...+. +++++.|||+||..|+.+|+..       ...||+|+..+...++.
T Consensus        13 ~~C~IC~~~~~-~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   69 (79)
T 2egp_A           13 VTCPICLELLT-EPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQ   69 (79)
T ss_dssp             CEETTTTEECS-SCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGGG
T ss_pred             CCCcCCCcccC-CeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhCC
Confidence            47999999986 5889999999999999999875       67899999999876553

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.08  E-value=6.9e-11  Score=85.83  Aligned_cols=52  Identities=25%  Similarity=0.590  Sum_probs=42.8

Q ss_pred             CccccCcc-cccCC---cEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCCcc
Q 022126            1 MRCNACWR-ELEGR---AISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~-~l~~~---~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~div~   52 (302)
                      +.|+||+. .+.+.   ++++.|||+||..|+.+++.. ...||+|++.+...++.+
T Consensus         4 ~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   60 (65)
T 1g25_A            4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRV   60 (65)
T ss_dssp             TCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCEE
T ss_pred             CcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCcccccccee
Confidence            46999999 66542   268999999999999999764 578999999998877654

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=99.07  E-value=5.7e-11  Score=88.78  Aligned_cols=48  Identities=25%  Similarity=0.508  Sum_probs=41.1

Q ss_pred             CccccCcccccCCcEEec-CCccccHHHHHhhhcCC--CCCCCCccccccCC
Q 022126            1 MRCNACWRELEGRAISTT-CGHLLCTEDANKILSND--AACPICDQVLSKSL   49 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~-CGHiFC~~Ci~~~~~~~--~~CPvC~~~l~~~d   49 (302)
                      +.|+||...+. +++++. |||+||..|+..|+...  ..||+|++.+...+
T Consensus        16 ~~C~IC~~~~~-~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           16 LLCLICKDIMT-DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             GSCSSSCCCCT-TCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCcCCChHHh-CCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            47999999886 689999 99999999999998753  79999999865544

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens}

Probab=99.06  E-value=9.9e-11  Score=95.43  Aligned_cols=46  Identities=26%  Similarity=0.633  Sum_probs=41.2

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-CCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~   47 (302)
                      +.|+||...+. +|+++.|||+||..|+..|+.. ...||+|++.+..
T Consensus        53 ~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           53 FQCICCQELVF-RPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             TBCTTTSSBCS-SEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCcCChHHc-CcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            47999999986 6999999999999999999875 5599999999876

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=99.06  E-value=8.8e-11  Score=92.04  Aligned_cols=49  Identities=27%  Similarity=0.644  Sum_probs=42.9

Q ss_pred             CccccCcccccCCcEEe-cCCccccHHHHHhhhcCCCCCCCCccccccCCC
Q 022126            1 MRCNACWRELEGRAIST-TCGHLLCTEDANKILSNDAACPICDQVLSKSLM   50 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT-~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~di   50 (302)
                      +.|+||...+. +++++ .|||+||..|+.+|+.....||+|+..+...++
T Consensus        23 ~~C~IC~~~~~-~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l   72 (99)
T 2y43_A           23 LRCGICFEYFN-IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDL   72 (99)
T ss_dssp             TBCTTTCSBCS-SEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGC
T ss_pred             CCcccCChhhC-CcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhhC
Confidence            57999999986 58777 899999999999999888999999998876444

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.05  E-value=1.1e-10  Score=88.79  Aligned_cols=50  Identities=24%  Similarity=0.712  Sum_probs=43.0

Q ss_pred             CccccCcccccC---CcEEecCCccccHHHHHhhhcCC---CCCCCCccccccCCC
Q 022126            1 MRCNACWRELEG---RAISTTCGHLLCTEDANKILSND---AACPICDQVLSKSLM   50 (302)
Q Consensus         1 l~CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~~~~---~~CPvC~~~l~~~di   50 (302)
                      +.|+||+..+.+   .++++.|||+||..|+.+|+...   ..||.|++.+...++
T Consensus        16 ~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~i   71 (88)
T 2ct2_A           16 LECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSL   71 (88)
T ss_dssp             CBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSST
T ss_pred             CCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchhH
Confidence            479999999863   28999999999999999998754   799999999877654

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=99.04  E-value=5.5e-11  Score=107.26  Aligned_cols=51  Identities=14%  Similarity=0.199  Sum_probs=44.0

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~div~   52 (302)
                      |.|+||...+. +||+|.|||+||..||.+|+.. ..+||+|+.+++..++++
T Consensus       209 ~~c~i~~~~~~-dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~~  260 (281)
T 2c2l_A          209 LCGKISFELMR-EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIP  260 (281)
T ss_dssp             TBCTTTCSBCS-SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEE
T ss_pred             cCCcCcCCHhc-CCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCcc
Confidence            67999999986 6999999999999999999975 455999999998665544

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.04  E-value=7.3e-11  Score=88.68  Aligned_cols=51  Identities=24%  Similarity=0.663  Sum_probs=44.1

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC------CCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN------DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~------~~~CPvC~~~l~~~div~   52 (302)
                      +.|+||+..+. +++++.|||+||..|+..|+..      ...||.|++.+...++.+
T Consensus        20 ~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~   76 (85)
T 2ecv_A           20 VTCPICLELLT-QPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRP   76 (85)
T ss_dssp             CCCTTTCSCCS-SCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCCC
T ss_pred             CCCCCCCcccC-CceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcCc
Confidence            47999999986 5888999999999999999865      789999999998766543

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.03  E-value=9.9e-11  Score=92.94  Aligned_cols=51  Identities=25%  Similarity=0.725  Sum_probs=43.5

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCC---CCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSND---AACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~---~~CPvC~~~l~~~div~   52 (302)
                      +.|+||+..+. .++++.|||+||..|+..|+...   ..||+|+..+...++..
T Consensus        22 ~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~~   75 (112)
T 1jm7_A           22 LECPICLELIK-EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQE   75 (112)
T ss_dssp             TSCSSSCCCCS-SCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBC
T ss_pred             CCCcccChhhc-CeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcCc
Confidence            47999999886 68899999999999999998753   58999999998766544

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A

Probab=99.02  E-value=2.7e-10  Score=90.69  Aligned_cols=47  Identities=28%  Similarity=0.569  Sum_probs=42.1

Q ss_pred             CccccCcccccCCcEEe-cCCccccHHHHHhhhcCCCCCCCCccccccC
Q 022126            1 MRCNACWRELEGRAIST-TCGHLLCTEDANKILSNDAACPICDQVLSKS   48 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT-~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~   48 (302)
                      +.|+||...+. +++++ .|||+||..|+..|+.....||+|+..+...
T Consensus        16 ~~C~IC~~~~~-~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           16 LMCVLCGGYFI-DATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             TBCTTTSSBCS-SEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CCCccCChHHh-CcCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            57999999986 58887 9999999999999998889999999988754

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.02  E-value=9.3e-11  Score=85.09  Aligned_cols=47  Identities=28%  Similarity=0.735  Sum_probs=40.4

Q ss_pred             CccccCcccccC------CcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEG------RAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~------~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      +.|+||+..+.+      .++++.|||+||..|+.+|+.....||+|++.+..
T Consensus        16 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           16 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            469999998853      12899999999999999999888899999998753

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=99.02  E-value=1.3e-10  Score=89.67  Aligned_cols=45  Identities=27%  Similarity=0.584  Sum_probs=39.6

Q ss_pred             CccccCcccccCCcEEec-CCccccHHHHHhhhcC--CCCCCCCccccc
Q 022126            1 MRCNACWRELEGRAISTT-CGHLLCTEDANKILSN--DAACPICDQVLS   46 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~-CGHiFC~~Ci~~~~~~--~~~CPvC~~~l~   46 (302)
                      +.|+||...+. +|+++. |||+||..|+..|+..  ...||+|++.+.
T Consensus        14 ~~C~IC~~~~~-~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           14 LLCLICKDIMT-DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             TEETTTTEECS-SCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CCCCCCChhhc-CceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            57999999886 699999 9999999999999863  469999999874

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.01  E-value=1.3e-10  Score=87.06  Aligned_cols=52  Identities=19%  Similarity=0.462  Sum_probs=44.4

Q ss_pred             CccccCcccccC--CcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEG--RAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~--~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~   52 (302)
                      +.|+||+..+..  ..+++.|||+||..|+.+|+.....||+|++.+...++..
T Consensus        16 ~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   69 (78)
T 2ect_A           16 LECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTAT   69 (78)
T ss_dssp             CCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCC
T ss_pred             CCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCC
Confidence            469999998863  3467799999999999999988899999999998876654

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.00  E-value=1.9e-10  Score=92.99  Aligned_cols=57  Identities=26%  Similarity=0.686  Sum_probs=48.5

Q ss_pred             CccccCcccccCCc-------EEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcccccCCC
Q 022126            1 MRCNACWRELEGRA-------ISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDINPN   58 (302)
Q Consensus         1 l~CNiC~~~l~~~~-------vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~~LnPs   58 (302)
                      +.|+||+..+.+ +       +++.|||+||..|+.+|+.....||+|++.+...++.++.++..
T Consensus         8 ~~C~IC~~~~~~-~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~l~i~~~   71 (133)
T 4ap4_A            8 VSCPICMDGYSE-IVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYIGSG   71 (133)
T ss_dssp             CBCTTTCCBHHH-HHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCEEECBCSSS
T ss_pred             CCCcccChhhhC-ccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccccccccCCC
Confidence            579999998863 4       99999999999999999998899999999998877766555433

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens}

Probab=98.99  E-value=2.7e-10  Score=96.78  Aligned_cols=47  Identities=21%  Similarity=0.587  Sum_probs=41.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCC-CCCCCCccccccC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSND-AACPICDQVLSKS   48 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~-~~CPvC~~~l~~~   48 (302)
                      +.|+||...+. +||+|.|||+||..|+..|+... ..||+|+..+...
T Consensus        79 ~~C~IC~~~~~-~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           79 FMCVCCQELVY-QPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             TBCTTTSSBCS-SEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CEeecCChhhc-CCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            57999999886 69999999999999999999764 5899999998765

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.99  E-value=2.6e-10  Score=82.12  Aligned_cols=40  Identities=28%  Similarity=0.737  Sum_probs=35.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc---CCCCCCCC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS---NDAACPIC   41 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~---~~~~CPvC   41 (302)
                      +.|+||+..+. +++++.|||+||..|+.+|+.   ....||+|
T Consensus        21 ~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           21 VICPICLDILQ-KPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CBCTTTCSBCS-SCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CCCCcCCchhC-CeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            47999999986 699999999999999999987   46789998

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.98  E-value=1.4e-10  Score=85.09  Aligned_cols=47  Identities=21%  Similarity=0.535  Sum_probs=42.3

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSL   49 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~d   49 (302)
                      +.|+||+..+.+  +++.|||+||..|+.+|+.....||+|++.+...+
T Consensus        16 ~~C~IC~~~~~~--~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           16 EECCICMDGRAD--LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCSSSCCSCCS--EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCeeCCcCccC--cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            469999999875  89999999999999999988899999999987654

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1

Probab=98.98  E-value=2.6e-10  Score=91.72  Aligned_cols=51  Identities=24%  Similarity=0.514  Sum_probs=44.5

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~div~   52 (302)
                      +.|+||...+. +|+++.|||+||..|+.+|+.. ...||+|+..+...+++.
T Consensus        24 ~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   75 (116)
T 1rmd_A           24 ISCQICEHILA-DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (116)
T ss_dssp             TBCTTTCSBCS-SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             CCCCCCCcHhc-CcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhccc
Confidence            57999999886 6999999999999999999876 779999999988766543

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=98.95  E-value=2.4e-10  Score=83.20  Aligned_cols=46  Identities=20%  Similarity=0.627  Sum_probs=41.3

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      .|+||+..+.+.++++.|||+||..|+.+|+.....||+|++.+..
T Consensus         7 ~C~IC~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            7 RCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCeeCCccccCCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            6999999987556899999999999999999888999999998864

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A

Probab=98.95  E-value=2.4e-10  Score=92.61  Aligned_cols=50  Identities=26%  Similarity=0.624  Sum_probs=42.9

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCC-CCCCCCccccccCCCc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSND-AACPICDQVLSKSLMK   51 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~-~~CPvC~~~l~~~div   51 (302)
                      +.|+||...+. .++++.|||+||..|+.+|+... ..||+|+..+...+++
T Consensus        19 ~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~   69 (118)
T 3hct_A           19 YECPICLMALR-EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLF   69 (118)
T ss_dssp             GBCTTTCSBCS-SEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCE
T ss_pred             CCCCcCChhhc-CeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHhcc
Confidence            47999999886 69999999999999999998764 4999999998765543

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens}

Probab=98.95  E-value=4.6e-10  Score=82.07  Aligned_cols=46  Identities=26%  Similarity=0.557  Sum_probs=40.6

Q ss_pred             ccccCccccc--CCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            2 RCNACWRELE--GRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~--~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      .|+||+..+.  ..++++.|||+||..|+.+|+.....||+|++.+..
T Consensus        16 ~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   63 (69)
T 2kiz_A           16 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEA   63 (69)
T ss_dssp             SBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCS
T ss_pred             CCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccC
Confidence            6999999885  357889999999999999999888899999998764

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.94  E-value=2.9e-10  Score=89.20  Aligned_cols=51  Identities=22%  Similarity=0.561  Sum_probs=42.4

Q ss_pred             CccccCcccccCCcEEec-CCccccHHHHHhhhcC------CCCCCC--Cccc-cccCCCcc
Q 022126            1 MRCNACWRELEGRAISTT-CGHLLCTEDANKILSN------DAACPI--CDQV-LSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~-CGHiFC~~Ci~~~~~~------~~~CPv--C~~~-l~~~div~   52 (302)
                      |.|+||...|. +||++. |||+||..||..||..      ..+||+  |.+. +...++++
T Consensus         8 ~~CPI~~~~~~-dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L~p   68 (94)
T 2yu4_A            8 FTCPITKEEMK-KPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLIQ   68 (94)
T ss_dssp             CBCTTTCSBCS-SEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGEEE
T ss_pred             eECcCcCchhc-CCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhCcC
Confidence            68999999986 699995 9999999999999864      368999  8877 76655543

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=98.93  E-value=3.5e-10  Score=78.90  Aligned_cols=45  Identities=29%  Similarity=0.623  Sum_probs=39.9

Q ss_pred             ccccCcccccC---CcEEecCCccccHHHHHhhhcCCCCCCCCccccc
Q 022126            2 RCNACWRELEG---RAISTTCGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      .|+||+..+.+   .++++.|||+||..|+.+|+.....||+|++.+.
T Consensus         7 ~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            7 GCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             SCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             cCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            69999998853   4788999999999999999988899999999764

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B

Probab=98.92  E-value=4.5e-10  Score=95.77  Aligned_cols=46  Identities=26%  Similarity=0.661  Sum_probs=40.7

Q ss_pred             CccccCcccccCCcEEe-cCCccccHHHHHhhhcC-CCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAIST-TCGHLLCTEDANKILSN-DAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT-~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~   47 (302)
                      +.|+||...+. .++++ .|||+||..|+.+|+.. ...||+|+..+..
T Consensus        55 ~~C~IC~~~~~-~p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           55 LMCPICLDMLK-NTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HBCTTTSSBCS-SEEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCcccChHhh-CcCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            36999999986 58877 99999999999999986 7889999998864

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.91  E-value=4.6e-10  Score=98.75  Aligned_cols=51  Identities=14%  Similarity=0.192  Sum_probs=44.3

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~div~   52 (302)
                      |.|+||...+. +||++.|||+||..||..|+.. ..+||+|+.+++..++++
T Consensus       107 f~CPI~~elm~-DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~p  158 (179)
T 2f42_A          107 LCGKISFELMR-EPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIP  158 (179)
T ss_dssp             GBCTTTCSBCS-SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEE
T ss_pred             hcccCccccCC-CCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcc
Confidence            57999999996 6999999999999999999975 457999999998766554

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, CHR protein, DNA repair, metal-binding, nucleus; 2.12A {Homo sapiens}

Probab=98.91  E-value=2.6e-10  Score=91.68  Aligned_cols=46  Identities=24%  Similarity=0.652  Sum_probs=40.7

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-CCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~   47 (302)
                      +.|+||+..+. +|+++.|||+||..|+.+|+.. ...||.|++.+..
T Consensus        16 ~~C~iC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           16 CQCGICMEILV-EPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HBCTTTCSBCS-SCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCccCCcccC-ceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            46999999886 6999999999999999999876 7789999998763

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.90  E-value=6.4e-10  Score=78.25  Aligned_cols=40  Identities=28%  Similarity=0.791  Sum_probs=35.0

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc---CCCCCCCC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS---NDAACPIC   41 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~---~~~~CPvC   41 (302)
                      +.|+||+..+. +++++.|||+||..|+.+|+.   ....||+|
T Consensus        16 ~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           16 ASCSVCLEYLK-EPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CBCSSSCCBCS-SCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             CCCccCCcccC-ccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            47999999986 588999999999999999954   46789998

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B

Probab=98.90  E-value=1.1e-09  Score=83.73  Aligned_cols=56  Identities=20%  Similarity=0.442  Sum_probs=43.8

Q ss_pred             CccccCccccc-CCcEEec--CCccccHHHHHhhhcC-CCCCCCCccccccCCCcccccC
Q 022126            1 MRCNACWRELE-GRAISTT--CGHLLCTEDANKILSN-DAACPICDQVLSKSLMKPVDIN   56 (302)
Q Consensus         1 l~CNiC~~~l~-~~~vvT~--CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~div~~~Ln   56 (302)
                      +.|+||...++ .++++..  |||.||..|+.++|.. ...||.|++.+...++....+.
T Consensus        12 ~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~~~~~~   71 (78)
T 1e4u_A           12 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVYKPLS   71 (78)
T ss_dssp             CBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSCCCSCC
T ss_pred             CcCCccCccCccccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchhhccCC
Confidence            46999999885 2344544  9999999999999854 6789999999988776554443

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.89  E-value=3.6e-10  Score=91.44  Aligned_cols=47  Identities=21%  Similarity=0.633  Sum_probs=40.5

Q ss_pred             CccccCcccccCCcEEe-cCCccccHHHHHhhhcCCCCCCCCccccccCCC
Q 022126            1 MRCNACWRELEGRAIST-TCGHLLCTEDANKILSNDAACPICDQVLSKSLM   50 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT-~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~di   50 (302)
                      +.|+||...+. +||++ .|||+||..|+..|+.  ..||+|++.+...++
T Consensus        23 ~~C~IC~~~~~-~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~   70 (117)
T 1jm7_B           23 LRCSRCTNILR-EPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDL   70 (117)
T ss_dssp             TSCSSSCSCCS-SCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSC
T ss_pred             CCCCCCChHhh-CccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCccccc
Confidence            57999999886 58888 9999999999999986  889999998865443

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.86  E-value=1.5e-09  Score=80.42  Aligned_cols=46  Identities=20%  Similarity=0.462  Sum_probs=39.7

Q ss_pred             ccccCcccccC--CcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            2 RCNACWRELEG--RAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~--~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      .|+||+..+..  ..+++.|||+||..|+.+|+.....||+|++.+..
T Consensus        17 ~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2ep4_A           17 LCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQ   64 (74)
T ss_dssp             BCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSS
T ss_pred             CCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCccccc
Confidence            69999999863  35566999999999999999888899999998764

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=98.85  E-value=1.3e-09  Score=76.09  Aligned_cols=46  Identities=30%  Similarity=0.663  Sum_probs=38.9

Q ss_pred             CccccCcccccC--CcEEec-CCccccHHHHHhhhcCCCCCCCCccccc
Q 022126            1 MRCNACWRELEG--RAISTT-CGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         1 l~CNiC~~~l~~--~~vvT~-CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      ..|+||+..+..  .++++. |||+||..|+.+|+.....||+|++.+.
T Consensus         6 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            6 VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            369999999863  356665 9999999999999988899999998753

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=98.84  E-value=1.3e-09  Score=79.64  Aligned_cols=54  Identities=13%  Similarity=0.164  Sum_probs=48.7

Q ss_pred             CccccCcccccCCcEEe-cCCccccHHHHHhhhcCCCCCCCCccccccCCCccccc
Q 022126            1 MRCNACWRELEGRAIST-TCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPVDI   55 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT-~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~~L   55 (302)
                      |.|+||.+.+. +||++ .|||+||+.||.+|+....+||+++.+|+..+++++..
T Consensus         4 ~~CpIs~~~m~-dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Lip~~~   58 (61)
T 2bay_A            4 MLCAISGKVPR-RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIVP   58 (61)
T ss_dssp             CCCTTTCSCCS-SEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEECCC
T ss_pred             EEecCCCCCCC-CCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcEECcc
Confidence            68999999996 69999 99999999999999987678999999999999887654

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}

Probab=98.84  E-value=1.5e-09  Score=84.32  Aligned_cols=45  Identities=22%  Similarity=0.513  Sum_probs=39.5

Q ss_pred             ccccCcccccC--CcEEecCCccccHHHHHhhhcCCCCCCCCccccc
Q 022126            2 RCNACWRELEG--RAISTTCGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~--~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      .|.||+..+..  .++++.|||+||..|+..|+.....||+|++.+.
T Consensus        42 ~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   88 (91)
T 2l0b_A           42 CCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFP   88 (91)
T ss_dssp             EETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSS
T ss_pred             CCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCC
Confidence            59999998852  3667899999999999999988889999999875

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=98.81  E-value=1.2e-09  Score=88.10  Aligned_cols=53  Identities=26%  Similarity=0.708  Sum_probs=45.2

Q ss_pred             CccccCcccccC------CcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCccc
Q 022126            1 MRCNACWRELEG------RAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPV   53 (302)
Q Consensus         1 l~CNiC~~~l~~------~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~   53 (302)
                      +.|+||...+..      ..+++.|||+||..|+.+|+.....||+|++.+..+++.++
T Consensus        73 ~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~  131 (133)
T 4ap4_A           73 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI  131 (133)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGEEEE
T ss_pred             CCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhcceee
Confidence            368899988752      23899999999999999999989999999999998877654

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.80  E-value=1.4e-09  Score=80.97  Aligned_cols=46  Identities=24%  Similarity=0.502  Sum_probs=39.6

Q ss_pred             ccccCcccccC--CcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            2 RCNACWRELEG--RAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~--~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      .|+||+..+..  ..+++.|||+||..|+.+|+.....||+|++.+..
T Consensus        25 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~   72 (75)
T 1x4j_A           25 LCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGP   72 (75)
T ss_dssp             EETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCC
Confidence            59999998863  24678899999999999999888899999998754

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens}

Probab=98.78  E-value=1.6e-09  Score=91.18  Aligned_cols=46  Identities=30%  Similarity=0.577  Sum_probs=40.0

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCC-CCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSND-AACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~-~~CPvC~~~l~~   47 (302)
                      +.|+||...+. .||+|.|||+||..|+.+|+... ..||+|+..+..
T Consensus        32 ~~C~IC~~~~~-~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           32 YLCSACRNVLR-RPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             GBCTTTCSBCS-SEEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             cCCCCCChhhc-CcEECCCCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            47999999986 69999999999999999998754 589999997643

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1

Probab=98.77  E-value=3e-09  Score=84.95  Aligned_cols=46  Identities=20%  Similarity=0.429  Sum_probs=37.7

Q ss_pred             ccccCcccccC-----------------CcEEecCCccccHHHHHhhh-----cCCCCCCCCcccccc
Q 022126            2 RCNACWRELEG-----------------RAISTTCGHLLCTEDANKIL-----SNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~-----------------~~vvT~CGHiFC~~Ci~~~~-----~~~~~CPvC~~~l~~   47 (302)
                      .|+||+..|..                 ..+++.|||+||..||..|+     .....||+|++.+..
T Consensus        27 ~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~   94 (114)
T 1v87_A           27 DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE   94 (114)
T ss_dssp             EETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSS
T ss_pred             cCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCC
Confidence            59999999853                 12278899999999999998     346799999998864

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens}

Probab=98.76  E-value=2.5e-09  Score=91.46  Aligned_cols=51  Identities=27%  Similarity=0.664  Sum_probs=43.6

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~div~   52 (302)
                      |.|+||...+. .||++.|||+||..|+.+|+.. ...||+|+..+...++++
T Consensus        19 ~~C~IC~~~~~-~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   70 (170)
T 3hcs_A           19 YECPICLMALR-EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFP   70 (170)
T ss_dssp             GBCTTTCSBCS-SEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEE
T ss_pred             CCCCCCChhhc-CcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhhhhh
Confidence            57999999986 6999999999999999999875 459999999987765543

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.74  E-value=4.9e-09  Score=79.88  Aligned_cols=47  Identities=17%  Similarity=0.413  Sum_probs=37.5

Q ss_pred             ccccCcccccC-------------CcE-EecCCccccHHHHHhhhcCCCCCCCCccccccC
Q 022126            2 RCNACWRELEG-------------RAI-STTCGHLLCTEDANKILSNDAACPICDQVLSKS   48 (302)
Q Consensus         2 ~CNiC~~~l~~-------------~~v-vT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~   48 (302)
                      .|.||+..+.+             .++ ++.|||+|+..||.+|+....+||+|++.+...
T Consensus        17 ~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           17 TCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            47888887743             144 445999999999999999888999999987543

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.72  E-value=1.7e-09  Score=76.92  Aligned_cols=43  Identities=28%  Similarity=0.615  Sum_probs=37.4

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      +.|.||...+. +++++.|||+||..|+..   ....||+|++.+..
T Consensus         7 ~~C~IC~~~~~-~p~~l~CgH~fC~~Ci~~---~~~~CP~Cr~~~~~   49 (56)
T 1bor_A            7 LRCQQCQAEAK-CPKLLPCLHTLCSGCLEA---SGMQCPICQAPWPL   49 (56)
T ss_dssp             SSCSSSCSSCB-CCSCSTTSCCSBTTTCSS---SSSSCSSCCSSSSC
T ss_pred             CCceEeCCccC-CeEEcCCCCcccHHHHcc---CCCCCCcCCcEeec
Confidence            57999999886 589999999999999877   36789999998764

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=98.69  E-value=5.2e-09  Score=97.12  Aligned_cols=51  Identities=22%  Similarity=0.490  Sum_probs=43.2

Q ss_pred             CccccCcccccCCcEE-ecCCccccHHHHHhhhcC--CCCCCC--CccccccCCCcc
Q 022126            1 MRCNACWRELEGRAIS-TTCGHLLCTEDANKILSN--DAACPI--CDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vv-T~CGHiFC~~Ci~~~~~~--~~~CPv--C~~~l~~~div~   52 (302)
                      |.|+||...|. +||+ +.|||+||..||.++|..  ...||+  |++.+...++++
T Consensus       182 l~CPIcl~~f~-DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~p  237 (267)
T 3htk_C          182 LTCPITCKPYE-APLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVR  237 (267)
T ss_dssp             SBCTTTSSBCS-SEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEE
T ss_pred             eECcCccCccc-CCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCc
Confidence            68999999996 6987 499999999999999975  468999  999887666544

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=98.62  E-value=1.5e-08  Score=75.91  Aligned_cols=42  Identities=29%  Similarity=0.704  Sum_probs=37.4

Q ss_pred             CccccCcccccCCcEEecCCcc-ccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHL-LCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHi-FC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      +.|.||+..+. +++++.|||. ||..|+.++    ..||+|++.+..
T Consensus        25 ~~C~iC~~~~~-~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           25 KLCKICMDRNI-AIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             TBCTTTSSSBC-CEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCC-CEEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            46999999885 6999999999 999999887    799999998865

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.53  E-value=3.6e-08  Score=73.79  Aligned_cols=41  Identities=29%  Similarity=0.732  Sum_probs=36.0

Q ss_pred             ccccCcccccCCcEEecCCcc-ccHHHHHhhhcCCCCCCCCcccccc
Q 022126            2 RCNACWRELEGRAISTTCGHL-LCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHi-FC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      .|.||+..+. +++++.|||. ||..|+.+.    ..||+|+..+..
T Consensus        27 ~C~IC~~~~~-~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   68 (75)
T 2ecg_A           27 LCKICMDRNI-AIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   68 (75)
T ss_dssp             SCSSSCSSCC-CBCCSSSCCCCBCHHHHHHC----SBCTTTCCBCCC
T ss_pred             CCCcCCCCCC-CEEEecCCCHHHHHHHhhCC----CCCccCCceecC
Confidence            6999999885 6899999999 999999753    789999999875

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=98.49  E-value=5.8e-08  Score=70.75  Aligned_cols=45  Identities=27%  Similarity=0.592  Sum_probs=38.7

Q ss_pred             ccccCcccccCCcEEe--cCCcc-ccHHHHHhhhcCCCCCCCCcccccc
Q 022126            2 RCNACWRELEGRAIST--TCGHL-LCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT--~CGHi-FC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      .|.||+.... ++++.  .|||. ||..|+.+++.....||+|++++..
T Consensus         9 ~C~IC~~~~~-~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   56 (63)
T 2vje_B            9 PCSLCEKRPR-DGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQL   56 (63)
T ss_dssp             BCTTTSSSBS-CEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCCE
T ss_pred             CCcccCCcCC-CeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhhc
Confidence            5999999875 46666  99998 9999999998888899999998853

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A

Probab=98.48  E-value=9.1e-08  Score=77.15  Aligned_cols=45  Identities=16%  Similarity=0.390  Sum_probs=38.4

Q ss_pred             ccccCcccccCC-----------------cEEecCCccccHHHHHhhhcCCCCCCCCccccc
Q 022126            2 RCNACWRELEGR-----------------AISTTCGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~~-----------------~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      .|.||+..|.+.                 .+++.|||+|+..||..|+....+||+|++.+.
T Consensus        39 ~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           39 NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            488999887532                 456889999999999999998999999999764

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=98.47  E-value=6.4e-08  Score=70.75  Aligned_cols=44  Identities=27%  Similarity=0.610  Sum_probs=38.7

Q ss_pred             ccccCcccccCCcEEe--cCCcc-ccHHHHHhhhcCCCCCCCCccccc
Q 022126            2 RCNACWRELEGRAIST--TCGHL-LCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT--~CGHi-FC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      .|.||+.... ++++.  .|||. ||..|+.+++.....||+|++.+.
T Consensus        10 ~C~IC~~~~~-~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A           10 PCVICQGRPK-NGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             CCTTTSSSCS-CEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CCCcCCCCCC-CEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            5999999876 46766  99999 899999999888889999999875

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.35  E-value=5.8e-08  Score=75.46  Aligned_cols=44  Identities=20%  Similarity=0.536  Sum_probs=34.4

Q ss_pred             CccccCcccccCCcEE--ecCCccccHHHHHhhhcC--------CCCCCC--Cccc
Q 022126            1 MRCNACWRELEGRAIS--TTCGHLLCTEDANKILSN--------DAACPI--CDQV   44 (302)
Q Consensus         1 l~CNiC~~~l~~~~vv--T~CGHiFC~~Ci~~~~~~--------~~~CPv--C~~~   44 (302)
                      +.|+||+..+.....+  +.|||.||..|+..++..        ...||.  |+..
T Consensus         6 ~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            6 SGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             CCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             cCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            5799999988643222  369999999999998752        247999  9987

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=98.34  E-value=1.9e-07  Score=71.04  Aligned_cols=42  Identities=26%  Similarity=0.667  Sum_probs=36.9

Q ss_pred             ccccCcccccCCcEEecCCcc-ccHHHHHhhhcCCCCCCCCccccccC
Q 022126            2 RCNACWRELEGRAISTTCGHL-LCTEDANKILSNDAACPICDQVLSKS   48 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHi-FC~~Ci~~~~~~~~~CPvC~~~l~~~   48 (302)
                      .|.||+..+. +++++.|||. ||..|+..+    ..||+|+..+...
T Consensus        20 ~C~IC~~~~~-~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           20 LCMVCCEEEI-NSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             BCTTTSSSBC-CEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             EeEEeCcccC-cEEEECCCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            6999998875 6999999999 999999876    3999999998763

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}

Probab=98.22  E-value=1.6e-07  Score=77.26  Aligned_cols=45  Identities=16%  Similarity=0.405  Sum_probs=0.0

Q ss_pred             ccccCcccccC-----------------CcEEecCCccccHHHHHhhhcCCCCCCCCccccc
Q 022126            2 RCNACWRELEG-----------------RAISTTCGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~-----------------~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      .|.||+..|.+                 ..+.+.|||+|+..||.+|+.....||+|++.+.
T Consensus        50 ~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           50 NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             --------------------------------------------------------------
T ss_pred             cCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            48899988753                 1233689999999999999988899999999754

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.19  E-value=5.8e-07  Score=66.58  Aligned_cols=41  Identities=24%  Similarity=0.615  Sum_probs=35.9

Q ss_pred             ccccCcccccCCcEEecCCcc-ccHHHHHhhhcCCCCCCCCcccccc
Q 022126            2 RCNACWRELEGRAISTTCGHL-LCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHi-FC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      .|.||+.... +++++.|||. ||..|+...    ..||+|++.+..
T Consensus        17 ~C~IC~~~~~-~~v~~pCgH~~~C~~C~~~~----~~CP~CR~~i~~   58 (68)
T 2ea5_A           17 DCVVCQNGTV-NWVLLPCRHTCLCDGCVKYF----QQCPMCRQFVQE   58 (68)
T ss_dssp             CCSSSSSSCC-CCEETTTTBCCSCTTHHHHC----SSCTTTCCCCCC
T ss_pred             CCCCcCcCCC-CEEEECCCChhhhHHHHhcC----CCCCCCCcchhc
Confidence            6999998875 6999999999 999999853    789999998865

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=97.85  E-value=8e-06  Score=65.53  Aligned_cols=46  Identities=22%  Similarity=0.481  Sum_probs=40.1

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhc-CCCCCCCCcccccc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILS-NDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~-~~~~CPvC~~~l~~   47 (302)
                      -|.+|.-++....-+..|.|+||.+|+..+.+ .+..||.|+.++..
T Consensus         3 fC~~C~~Pi~iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEEEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            48899999976677999999999999999875 58899999998754

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.77  E-value=1.1e-05  Score=61.85  Aligned_cols=46  Identities=17%  Similarity=0.444  Sum_probs=39.1

Q ss_pred             ccccCccccc-CCcEEecCC-----ccccHHHHHhhhcC--CCCCCCCcccccc
Q 022126            2 RCNACWRELE-GRAISTTCG-----HLLCTEDANKILSN--DAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~-~~~vvT~CG-----HiFC~~Ci~~~~~~--~~~CPvC~~~l~~   47 (302)
                      .|.||+..+. +.++++.|+     |.|...|+.+|+..  ...||+|+..+..
T Consensus        17 ~C~IC~~~~~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~   70 (80)
T 2d8s_A           17 ICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIM   70 (80)
T ss_dssp             CCSSSCCCCCSSSCEECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCC
T ss_pred             CCeEcCccccCCCeeEeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeec
Confidence            5999998875 468899996     99999999999875  4699999998754

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.55  E-value=5.7e-05  Score=57.25  Aligned_cols=46  Identities=24%  Similarity=0.492  Sum_probs=37.8

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhcCC--CCCCCCcccccc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILSND--AACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~--~~CPvC~~~l~~   47 (302)
                      .|.||+..+...-.-..|+|.|=..|+.+||...  .+||.|++.+..
T Consensus        17 ~C~IC~~~i~~g~~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~   64 (74)
T 2ct0_A           17 ICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH   64 (74)
T ss_dssp             BCSSSCCBCSSSEECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCS
T ss_pred             cCcchhhHcccCCccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCC
Confidence            5999999886433334899999999999999765  899999998753

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=96.11  E-value=0.026  Score=46.41  Aligned_cols=69  Identities=17%  Similarity=0.304  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          111 MQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQEL----------QEKFSEKSRQKRKLDEMYDQLRSEYESMK  179 (302)
Q Consensus       111 L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~EL----------q~ky~EKsRq~~qLqelYdkLK~~~e~~~  179 (302)
                      ....|+..+.+++++++...+..+....|++.|+.++++|          +.+|.|-.++-+..++-|.+||..|..++
T Consensus        41 ~v~ql~~~i~~Le~eL~e~r~~~q~a~~e~e~Lr~e~~~l~~~~~~~~~~q~~~~e~E~kAqa~Eerf~KLKe~yteLr  119 (120)
T 3i00_A           41 VVLQLKGHVSELEADLAEQQHLRQQAADDCEFLRAELDELRRQREDTEKAQRSLSEIERKAQANEQRYSKLKEKYSELV  119 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCC----------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3445555666666666655444444455666666666666          77888888888899999999999887664

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=95.72  E-value=0.13  Score=39.55  Aligned_cols=56  Identities=16%  Similarity=0.324  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHH
Q 022126          121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSE-------KSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       121 e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~E-------KsRq~~qLqelYdkLK~~~e  176 (302)
                      ++++.|+.+-.++..++-|++.||.+|..|...-.+       ..++..+|++-...-..++.
T Consensus        10 qLE~KIq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~   72 (81)
T 2jee_A           10 KLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQ   72 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444555566666666666666555555       55666666665555555543

>3mq7_A Bone marrow stromal antigen 2; HIV, antiviral protein; 2.28A {Homo sapiens} PDB: 3mqc_A 3mqb_A 3mkx_A 3nwh_A 2xg7_A* 2x7a_A

Probab=95.10  E-value=0.13  Score=42.01  Aligned_cols=28  Identities=18%  Similarity=0.304  Sum_probs=10.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          147 KQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       147 n~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      ++||+.+..+=+.+++...+-...||++
T Consensus        73 vqeLqgEI~~Lnq~Lq~a~ae~erlr~~  100 (121)
T 3mq7_A           73 VEELEGEITTLNHKLQDASAEVERLRRE  100 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3333333333333333333333344444

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=94.95  E-value=0.014  Score=42.01  Aligned_cols=44  Identities=30%  Similarity=0.529  Sum_probs=35.1

Q ss_pred             ccccCcccccCCcEEecCC--c---cccHHHHHhhhcC--CCCCCCCccccc
Q 022126            2 RCNACWRELEGRAISTTCG--H---LLCTEDANKILSN--DAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CG--H---iFC~~Ci~~~~~~--~~~CPvC~~~l~   46 (302)
                      .|-||+... +.+++..|.  |   .|=..|+.+|+..  ...||+|+..+.
T Consensus         8 ~CrIC~~~~-~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            8 VCWICNEEL-GNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             EETTTTEEC-SCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             EeEEeecCC-CCceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            488999875 456788865  4   8899999999863  689999999764

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

Probab=94.77  E-value=0.22  Score=39.85  Aligned_cols=45  Identities=13%  Similarity=0.282  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          136 MEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKR  180 (302)
Q Consensus       136 me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~r  180 (302)
                      ++..++.+...+.+|++.|+||+|++.++.-.++.|+.++..++.
T Consensus        35 LKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~~lk~   79 (103)
T 4h22_A           35 LKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEVKE   79 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444455556666777888877777777777777766544

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

Probab=94.72  E-value=0.94  Score=35.71  Aligned_cols=71  Identities=10%  Similarity=0.185  Sum_probs=56.4

Q ss_pred             HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          106 QKCEAMQEK---FTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       106 eK~e~L~~~---l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      ++++.++..   ......+++..+..|++|++.++.+++.......+.+.++++..+.....+.-...|-+++.
T Consensus        23 drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~eld~~ee~L~ea~~kLee~ek~~~~aE~ev~~L~Rriq   96 (101)
T 3u1c_A           23 DRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTEDSRDQVLEELHKSEDSLLFAEENAAKAESEVASLNRRIQ   96 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444433   34566678888999999999999999999999999999999999888877777777777744

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=94.66  E-value=0.012  Score=45.51  Aligned_cols=31  Identities=23%  Similarity=0.446  Sum_probs=25.3

Q ss_pred             CccccCcccccCCcEE--ecCCccccHHHHHhh
Q 022126            1 MRCNACWRELEGRAIS--TTCGHLLCTEDANKI   31 (302)
Q Consensus         1 l~CNiC~~~l~~~~vv--T~CGHiFC~~Ci~~~   31 (302)
                      +.|.+|...+...|+.  ..|||.||..|+..+
T Consensus         4 ~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            4 VLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            4799999754446777  899999999999983

>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=94.46  E-value=0.79  Score=45.13  Aligned_cols=64  Identities=13%  Similarity=0.190  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRS  181 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rs  181 (302)
                      +..+....++..++.+++.+.+.+.+++++.++.+++++..++..++++-.+.+++++.++...
T Consensus       517 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~  580 (597)
T 3oja_B          517 RQAFKLRETQARRTEADAKQKETEDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAK  580 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hhhhhHHHHHHHHHhhhhhhcchhhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333334444444445555566666667777777777777777777777777777776555443

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

Probab=94.32  E-value=2  Score=41.26  Aligned_cols=18  Identities=22%  Similarity=0.270  Sum_probs=10.7

Q ss_pred             HhcC-CChHHHHHHHHHhh
Q 022126           65 AMAG-VSPQILMKSAYRSV   82 (302)
Q Consensus        65 vL~G-lsP~~Ime~a~RAi   82 (302)
                      ++.| .+|+.+++.+...+
T Consensus       364 vl~G~~t~eeal~~~~~~i  382 (471)
T 3mq9_A          364 AASGRQTVDEALKDAQTRI  382 (471)
T ss_dssp             HHHSSSCHHHHHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHH
Confidence            4555 57777775554443

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=93.77  E-value=2.7  Score=36.97  Aligned_cols=48  Identities=13%  Similarity=0.258  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q 022126          103 QCRQKCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQEL  150 (302)
Q Consensus       103 ~lreK~e~L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~EL  150 (302)
                      .+.+....|+..+...+.+++.....|+.++..+..|++..|.|+..+
T Consensus        35 EFqesSrELE~ELE~eL~~~Ek~~~~L~~~~~~L~~E~e~~k~K~~~~   82 (189)
T 2v71_A           35 EFQEGSRELEAELEAQLVQAEQRNRDLQADNQRLKYEVEALKEKLEHQ   82 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444455666666666666655555555555555555555544444

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

Probab=93.71  E-value=0.69  Score=38.62  Aligned_cols=48  Identities=13%  Similarity=0.198  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          127 QKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       127 ~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      +.|...+.+++.|+..|+.++.+++.++++-.+++.+|++-++.|..+
T Consensus        78 ~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~  125 (138)
T 3hnw_A           78 DSLSLDIENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKN  125 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333444444444444444444444444444444444444444443

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

Probab=92.66  E-value=2.8  Score=32.76  Aligned_cols=61  Identities=20%  Similarity=0.309  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          116 TEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       116 ~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      .....+++..+..+++|+..++.+++.......+++.++++..+...+-+.-...|-+++.
T Consensus        36 e~~~~~~E~ei~sL~kKiq~lE~eld~~~e~l~~a~~kLe~~ek~~~~AE~evasLnRriq   96 (101)
T 3u59_A           36 EDRCKQLEEEQQGLQKKLKGTEDEVEKYSESVKEAQEKLEQAEKKATDAEAEVASLNRRIQ   96 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456667788888999999999999999999999999999988888877777777777743

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

Probab=92.50  E-value=1.1  Score=37.43  Aligned_cols=50  Identities=16%  Similarity=0.211  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 022126          117 EKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDE  166 (302)
Q Consensus       117 ~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqe  166 (302)
                      ..+.+...++..|++++.+.+-+.+.+++++.+|++++.+=.++..+|+.
T Consensus        82 ~~l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~  131 (138)
T 3hnw_A           82 LDIENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLET  131 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444455555566666666666666666666666666666666666653

>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=92.35  E-value=2.5  Score=31.77  Aligned_cols=42  Identities=19%  Similarity=0.314  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSR  159 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsR  159 (302)
                      ...+++..+..|++|++.++.+++.......+.+.+|++..+
T Consensus        35 ~~~~~E~ev~~L~kKiq~lE~eld~~ee~l~~a~~kLeeaek   76 (81)
T 1ic2_A           35 RSKQLEDELVALQKKLKGTEDELDKYSESLKDAQEKLELADK   76 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555666666666666666666666666666666665544

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=91.94  E-value=0.084  Score=42.29  Aligned_cols=52  Identities=23%  Similarity=0.416  Sum_probs=41.9

Q ss_pred             CccccCccccc--CCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELE--GRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~--~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~   52 (302)
                      |.|..|.+.|.  +..+...=|.+||..|..+.+.....|-.|++++...+++.
T Consensus        33 F~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~~~~   86 (122)
T 1m3v_A           33 LKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGDVMV   86 (122)
T ss_dssp             HCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEESSS
T ss_pred             CCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchheEE
Confidence            57899999995  24566778999999999998766668999999998766543

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

Probab=91.86  E-value=1.9  Score=36.45  Aligned_cols=60  Identities=15%  Similarity=0.271  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          117 EKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       117 ~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      ..+.++...+..+..++..++.+++.++....+++..+.+...++.+++.-...++.++.
T Consensus        34 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (284)
T 1c1g_A           34 DRSKQLEDELVSLQKKLKATEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQ   93 (284)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445555555555555556666666666666666666555555555555555555443

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=91.72  E-value=3.3  Score=36.35  Aligned_cols=18  Identities=17%  Similarity=0.206  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 022126          159 RQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       159 Rq~~qLqelYdkLK~~~e  176 (302)
                      |+.+.+..-+..+..+++
T Consensus       123 r~~R~~~~SleD~e~kln  140 (189)
T 2v71_A          123 RAKRATIMSLEDFEQRLN  140 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHH
Confidence            333333333333433433

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

Probab=91.64  E-value=3.5  Score=32.91  Aligned_cols=64  Identities=6%  Similarity=0.185  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          113 EKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       113 ~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      .++++--..+.=+++.|+.++.+++....+++|++.|..+.++--.|.+..|+.-++.|+.++.
T Consensus        19 AQLDNEKsal~YqVdlLKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~~lk~~L~   82 (103)
T 4h22_A           19 AQLDNEKTNFMYQVDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEVKEALK   82 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444433344445666777778888888888888888888888888888888888888887743

>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=91.62  E-value=0.69  Score=34.93  Aligned_cols=43  Identities=7%  Similarity=0.241  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          133 CQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEY  175 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~  175 (302)
                      +..++.++....+....+-..+..-.|+++.|++-++++..++
T Consensus        22 ~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~ee~l   64 (81)
T 1ic2_A           22 AEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESL   64 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333333444444444444444443

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=91.57  E-value=1.6  Score=43.87  Aligned_cols=58  Identities=14%  Similarity=0.311  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH------------------------HHHHHHHHHHHHHHHhhc
Q 022126          128 KMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLD------------------------EMYDQLRSEYESMKRSAI  183 (302)
Q Consensus       128 kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLq------------------------elYdkLK~~~e~~~rsa~  183 (302)
                      .|.+++..|+.++++.-..+.-||..+++---+.++|+                        +-|+.+.++++++-...+
T Consensus       114 ELRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvDIdiqirsCKgsCsr~~~~~vd~~sY~~~QKQLeQv~a~dL  193 (562)
T 3ghg_A          114 DLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALAREVDLKDYEDQQKQLEQVIAKDL  193 (562)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGTBSCCCCCCCCHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccchheeecchHHHHHHHHHHHHHhhccc
Confidence            34455555555555555666666666666666666665                        457888899998877666


Q ss_pred             CC
Q 022126          184 QP  185 (302)
Q Consensus       184 ~~  185 (302)
                      .|
T Consensus       194 ~p  195 (562)
T 3ghg_A          194 LP  195 (562)
T ss_dssp             CC
T ss_pred             CC
Confidence            66

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=91.41  E-value=0.56  Score=45.42  Aligned_cols=57  Identities=16%  Similarity=0.321  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      ++.+++.++..++.+..+++.+++.++.++.+|.++|.+.....++|.+.+..||-+
T Consensus         4 ~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~rr~l~n~~~elkgn   60 (403)
T 4etp_A            4 KIAALKEKIAALKEKIAALKEKIKDTELGMKELNEILIKEETVRRTLHNELQELRGN   60 (403)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            455666667777777888888889999999999999998888888887777777655

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens}

Probab=91.35  E-value=0.21  Score=39.75  Aligned_cols=46  Identities=17%  Similarity=0.302  Sum_probs=39.0

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKS   48 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~   48 (302)
                      |.|..|.+.|.+..+...=|.++|..|..+.+  ...|..|++++...
T Consensus        31 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~--~~~C~~C~~~I~~~   76 (126)
T 2xqn_T           31 FCCFDCDSILAGEIYVMVNDKPVCKPCYVKNH--AVVCQGCHNAIDPE   76 (126)
T ss_dssp             SBCTTTCCBCTTSEEEEETTEEEEHHHHHHHS--CCBCTTTCSBCCTT
T ss_pred             CCcCCCCCCCCcCEEEeECCEEechHHhCcCc--CccCcccCCcCCcC
Confidence            67889999998777888889999999998763  56899999998754

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

Probab=91.24  E-value=4.9  Score=33.88  Aligned_cols=11  Identities=0%  Similarity=0.120  Sum_probs=4.0

Q ss_pred             HHHHHHHHHHH
Q 022126          121 QVHTAYQKMAK  131 (302)
Q Consensus       121 e~~s~~~kl~~  131 (302)
                      ++...+..+..
T Consensus        45 ~~~~~~~~~~~   55 (284)
T 1c1g_A           45 SLQKKLKATED   55 (284)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            33333333333

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

Probab=91.08  E-value=0.92  Score=54.37  Aligned_cols=61  Identities=13%  Similarity=0.271  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      ++.+++.++++.+.++.+.+.++..+..++++|+++|++..+++++|++-.+..+.+++.+
T Consensus      2015 ~l~~ae~~l~~~~~~L~~~~~~L~~le~~l~~L~~~~~~~~~ek~~L~~e~~~~~~kl~rA 2075 (3245)
T 3vkg_A         2015 EVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRS 2075 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445566666667777888888888999999999999999998888888887777665533

>1go4_E MAD1 (mitotic arrest deficient)-like 1; mitotic spindle checkpoint, cell cycle, mitosis, nuclear Pro; 2.05A {Homo sapiens} SCOP: h.1.22.1

Probab=90.25  E-value=2.6  Score=33.50  Aligned_cols=57  Identities=21%  Similarity=0.346  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH---------------------HHHHHHHHHHHHHHHHHHHHHHHh
Q 022126          125 AYQKMAKRCQMMEQEIESLSKDKQELQEKFSEK---------------------SRQKRKLDEMYDQLRSEYESMKRS  181 (302)
Q Consensus       125 ~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EK---------------------sRq~~qLqelYdkLK~~~e~~~rs  181 (302)
                      +|..+..++.+++.|.+.|++++.+|--+++-+                     +--+++.++..++|+.+++.+|..
T Consensus        13 ~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~~l~Gd~~~~~TKVlH~~~NPa~~a~~~~~~~~e~Lq~E~erLr~~   90 (100)
T 1go4_E           13 EADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAECERLRGL   90 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCSCCCTTTEEEEEESSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCccCeeeeecCChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566677777888888888888888877777541                     123445567777777777766654

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=90.20  E-value=5.6  Score=32.09  Aligned_cols=8  Identities=0%  Similarity=0.327  Sum_probs=2.9

Q ss_pred             HHHHHHHH
Q 022126          162 RKLDEMYD  169 (302)
Q Consensus       162 ~qLqelYd  169 (302)
                      .-++..||
T Consensus        80 eD~E~k~n   87 (111)
T 2v66_B           80 EDFEQRLN   87 (111)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            33333333

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

Probab=90.12  E-value=5.6  Score=34.32  Aligned_cols=59  Identities=19%  Similarity=0.344  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          113 EKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQL  171 (302)
Q Consensus       113 ~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkL  171 (302)
                      ..+...+..++.....|+.++..++.+.+.|.+++-.||..+.+--+-..+..+++..|
T Consensus        37 tEl~k~~~~~E~~~rELq~~~~~L~~~k~~Leke~~~LQa~L~qEr~~r~q~se~~~el   95 (168)
T 3o0z_A           37 TEMSKSISQLESLNRELQERNRILENSKSQTDKDYYQLQAILEAERRDRGHDSEMIGDL   95 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444555555555566666666777777777777777777766555555444444433

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=89.97  E-value=3.9  Score=39.38  Aligned_cols=9  Identities=22%  Similarity=0.575  Sum_probs=3.2

Q ss_pred             HHHhHHHHH
Q 022126          143 LSKDKQELQ  151 (302)
Q Consensus       143 LrKkn~ELq  151 (302)
                      ++++++.|+
T Consensus       447 ~~~~~~~~~  455 (487)
T 3oja_A          447 LAEENARLK  455 (487)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHhhhhh
Confidence            333333333

>3t98_B Nucleoporin NUP58/NUP45; NUP62 complex, nuclear import, coiled-coil, HE hairpin, FG-repeat, NPC, nuclear tranport, TRA channel, karyopherin; 2.50A {Rattus norvegicus} PDB: 2osz_A

Probab=89.87  E-value=4.5  Score=31.57  Aligned_cols=73  Identities=16%  Similarity=0.281  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022126          111 MQEKFTEKLEQVHTAYQKMAKRCQMMEQ----EIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSAI  183 (302)
Q Consensus       111 L~~~l~~ki~e~~s~~~kl~~kl~~me~----E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa~  183 (302)
                      +..+|++.+......|+.+++.+..+..    .-++|.+-.+.+.+-|-.=+-+...|++-.+.+|.+|-+.||...
T Consensus        13 lv~~fe~rL~~Yr~~IeelE~~L~s~s~~~~~Tpq~L~~~l~~~h~~FiaLAa~l~~lH~~V~~~Ke~Yl~~rr~~~   89 (93)
T 3t98_B           13 LVQQFEVQLQQYRQQIEELENHLATQANNSHITPQDLSMAMQKIYQTFVALAAQLQSIHENVKVLKEQYLSYRKMFL   89 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSCHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3444444555555555555544444332    125678888888888999999999999999999999999988755

>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=89.85  E-value=11  Score=36.73  Aligned_cols=30  Identities=10%  Similarity=0.202  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 022126          126 YQKMAKRCQMMEQEIESLSKDKQELQEKFS  155 (302)
Q Consensus       126 ~~kl~~kl~~me~E~e~LrKkn~ELq~ky~  155 (302)
                      +++++.+.+.++.+.+.++++.+++++.|+
T Consensus       511 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  540 (597)
T 3oja_B          511 FTHLKERQAFKLRETQARRTEADAKQKETE  540 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhhhhhHHHHHHHHHhhhhhhcchh
Confidence            333333444444444444444444444444

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

Probab=89.77  E-value=3.4  Score=37.09  Aligned_cols=54  Identities=19%  Similarity=0.204  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Q 022126          123 HTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSE--KSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       123 ~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~E--KsRq~~qLqelYdkLK~~~e  176 (302)
                      ..+++.+...+..++.+++.++.+....++++..  ..|++..|+.-.+.++.+..
T Consensus        52 ~~~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l~~v~~~kE~~aL~kEie~~~~~i~  107 (256)
T 3na7_A           52 EEEKLALKLQVSKNEQTLQDTNAKIASIQKKMSEIKSERELRSLNIEEDIAKERSN  107 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHH
Confidence            3333333333334444444444444444433332  23555555555555555543

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3

Probab=89.70  E-value=0.24  Score=37.70  Aligned_cols=46  Identities=17%  Similarity=0.457  Sum_probs=37.4

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKS   48 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~   48 (302)
                      |.|..|.+.|.+..+...=|.+||..|..+.+  ...|..|++.+...
T Consensus        34 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~--~~~C~~C~~~I~~~   79 (101)
T 2cup_A           34 FRCAKCLHPLANETFVAKDNKILCNKCTTRED--SPKCKGCFKAIVAG   79 (101)
T ss_dssp             CCCSSSCCCTTSSCCEEETTEEECHHHHTTCC--CCBCSSSCCBCCSS
T ss_pred             CcccccCCCCCcCeeECcCCEEEChhHhhhhc--CCccccCCCccccC
Confidence            67889999997666777789999999987653  56899999998743

>3iox_A AGI/II, PA; alpha helix, PPII helix, supersandwich fold, surface adhesin WALL, peptidoglycan-anchor, cell adhesion; HET: PMS; 1.80A {Streptococcus mutans} PDB: 3ipk_A* 1jmm_A

Probab=89.51  E-value=7  Score=38.98  Aligned_cols=45  Identities=11%  Similarity=0.172  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          131 KRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEY  175 (302)
Q Consensus       131 ~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~  175 (302)
                      .+-...++|.+..++.|.+.+.+|+.+-.|+++=-+-|++=+++|
T Consensus        41 a~n~~i~aeNeaikkrNa~aka~Ye~~l~kY~~dlakY~~~~AeY   85 (497)
T 3iox_A           41 AANAALTAENTAIKKRNADAKADYEAKLAKYQADLAKYQKDLADY   85 (497)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344557778888888888888888777666655545555544444

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=89.50  E-value=7.2  Score=31.44  Aligned_cols=56  Identities=16%  Similarity=0.121  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          121 QVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       121 e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +.++++..|+..+..+..+.+.+.+.+-+|-.+=-|=.|+.+-...-...+-++|.
T Consensus        32 e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDLER~~R~t~~SLeD~E~k~n   87 (111)
T 2v66_B           32 QSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIVSLEDFEQRLN   87 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHhhHHHHHHHHH
Confidence            33333444444444333333444333333333333334444444444444444444

>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=89.43  E-value=1.1  Score=33.71  Aligned_cols=31  Identities=23%  Similarity=0.238  Sum_probs=19.6

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          143 LSKDKQELQEKFSEKSRQKRKLDEMYDQLRS  173 (302)
Q Consensus       143 LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~  173 (302)
                      ....+.+|...+.||...+++|+.-+|++++
T Consensus        38 kd~~I~eLEk~L~ekd~eI~~LqseLDKfrS   68 (72)
T 3nmd_A           38 RDALIDELELELDQKDELIQMLQNELDKYRS   68 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3334566666677777777777766666643

>2wt7_B Transcription factor MAFB; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 2wty_A* 1k1v_A

Probab=88.90  E-value=3.9  Score=31.87  Aligned_cols=15  Identities=13%  Similarity=0.403  Sum_probs=11.4

Q ss_pred             HHHHhcCCChHHHHH
Q 022126           62 VNMAMAGVSPQILMK   76 (302)
Q Consensus        62 Kt~vL~GlsP~~Ime   76 (302)
                      .+..|.|++.+.|+.
T Consensus        11 LN~~L~gls~eev~~   25 (90)
T 2wt7_B           11 LNRHLRGFTKDEVIR   25 (90)
T ss_dssp             HHTTCTTCCHHHHHH
T ss_pred             HHHHHcCCCHHHHHH
Confidence            445678999999883

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=88.86  E-value=0.27  Score=52.77  Aligned_cols=51  Identities=10%  Similarity=0.063  Sum_probs=44.6

Q ss_pred             CccccCcccccCCcEEecCC-ccccHHHHHhhhcCCCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCG-HLLCTEDANKILSNDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CG-HiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~   52 (302)
                      |.|+|....+. +||++..| |.+=..+|.+|+....+||.-+.+|+..++++
T Consensus       892 F~cPIs~~lM~-DPVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~liP  943 (968)
T 3m62_A          892 FLDPLMYTIMK-DPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTP  943 (968)
T ss_dssp             GBCTTTCSBCS-SEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEE
T ss_pred             hCCcchhhHHh-CCeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCcccccc
Confidence            57999998886 69999998 58999999999988889999999998766655

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

Probab=88.56  E-value=2.8  Score=35.70  Aligned_cols=35  Identities=14%  Similarity=0.009  Sum_probs=15.5

Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          140 IESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       140 ~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      ++.++.++..|+-.+..-..+.++|+.-++.|..+
T Consensus        98 ~e~l~DEl~aLqlq~n~lE~kl~kLq~EN~~LV~R  132 (152)
T 3a7p_A           98 TERLNAALISGTIENNVLQQKLSDLKKEHSQLVAR  132 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444555545444433

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A

Probab=88.23  E-value=0.33  Score=38.69  Aligned_cols=49  Identities=27%  Similarity=0.602  Sum_probs=39.5

Q ss_pred             CccccCccccc--CCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCC
Q 022126            1 MRCNACWRELE--GRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSL   49 (302)
Q Consensus         1 l~CNiC~~~l~--~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~d   49 (302)
                      |.|..|.+.|.  +..+...=|.++|..|..+.+.....|..|++.+...+
T Consensus        30 F~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e   80 (131)
T 2xjy_A           30 LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYE   80 (131)
T ss_dssp             CBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECTTS
T ss_pred             cccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCccc
Confidence            67889999995  35677788999999999988755558999999886533

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

Probab=88.15  E-value=4.2  Score=34.56  Aligned_cols=58  Identities=17%  Similarity=0.286  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 022126          102 AQCRQKCEAMQEKFTEK---LEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSR  159 (302)
Q Consensus       102 ~~lreK~e~L~~~l~~k---i~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsR  159 (302)
                      .+++.++..++..+..|   ++.++.+|..|+-.+..++..+..|+++|.+|.+.|.++..
T Consensus        78 ~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE~kl~kLq~EN~~LV~RWM~rk~  138 (152)
T 3a7p_A           78 KSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKLSDLKKEHSQLVARWLKKTE  138 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45555666666555443   45566777777778888888999999999999888876543

>3swk_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural; 1.70A {Homo sapiens}

Probab=87.80  E-value=3  Score=31.95  Aligned_cols=52  Identities=19%  Similarity=0.347  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          125 AYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       125 ~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +++.+...-..+..|+++++...++++.||++--...+.+++-+..||+-++
T Consensus         8 qi~~l~~e~~~l~~e~dn~~~~~edfk~KyE~E~~~R~~~E~d~~~LrkdvD   59 (86)
T 3swk_A            8 QVDQLTNDKARVEVERDNLAEDIMRLREKLQEEMLQREEAENTLQSFRQDVD   59 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence            3333333334455556666666666666666666666666666655555443

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B

Probab=87.71  E-value=0.25  Score=42.36  Aligned_cols=48  Identities=29%  Similarity=0.699  Sum_probs=38.1

Q ss_pred             CccccCcccccC--CcEEecCCccccHHHHHhhhcCCCCCCCCccccccC
Q 022126            1 MRCNACWRELEG--RAISTTCGHLLCTEDANKILSNDAACPICDQVLSKS   48 (302)
Q Consensus         1 l~CNiC~~~l~~--~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~   48 (302)
                      |.|..|.+.|..  ..+...=|.+||..|..+.+.....|..|++.+...
T Consensus        33 F~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~   82 (188)
T 1rut_X           33 LKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPAS   82 (188)
T ss_dssp             CBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTT
T ss_pred             cccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccC
Confidence            678899998863  566777899999999988765444799999988653

>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus norvegicus}

Probab=87.25  E-value=9  Score=29.82  Aligned_cols=67  Identities=22%  Similarity=0.398  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          112 QEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       112 ~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      +..+-..+.+++..-..+...+..++.+.+.|..+-.++-..|.+-.+++..+++--++|..+|..+
T Consensus        20 E~~L~~eL~~lEke~~~l~~el~~le~E~~~L~~eE~~~w~eyn~~~~ql~e~~dE~~Sl~~q~~~~   86 (96)
T 3q8t_A           20 EERLIQELEDVEKNRKVVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSVENQMRYA   86 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455566667777777777778888888888888888888999999999999999999998887643

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=86.60  E-value=9.1  Score=29.24  Aligned_cols=13  Identities=31%  Similarity=0.565  Sum_probs=6.2

Q ss_pred             HHHHHHhHHHHHH
Q 022126          140 IESLSKDKQELQE  152 (302)
Q Consensus       140 ~e~LrKkn~ELq~  152 (302)
                      .+.|.++|+-|++
T Consensus        50 ~~~L~~en~qLk~   62 (81)
T 2jee_A           50 REELERENNHLKE   62 (81)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHH
Confidence            3335555555543

>1x79_B RAB GTPase binding effector protein 1; rabaptin5, GGA protein, GAT domain, intracellular trafficking, protein transport; 2.41A {Homo sapiens} SCOP: h.1.27.2

Probab=85.97  E-value=5.9  Score=32.04  Aligned_cols=34  Identities=15%  Similarity=0.102  Sum_probs=16.0

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          141 ESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSE  174 (302)
Q Consensus       141 e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~  174 (302)
                      +.-++++.+|...+..-...+..|+..|.++|+.
T Consensus        41 E~~k~qV~~L~~~~q~sE~~L~~Lqq~fsq~q~~   74 (112)
T 1x79_B           41 EDSSHQISALVLRAQASEILLEELQQGLSQAKRD   74 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444455445444443

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=85.17  E-value=15  Score=37.03  Aligned_cols=16  Identities=31%  Similarity=0.497  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHHH
Q 022126          103 QCRQKCEAMQEKFTEK  118 (302)
Q Consensus       103 ~lreK~e~L~~~l~~k  118 (302)
                      .|+.++++|++++..+
T Consensus       114 ELRRrIqyLKekVdnQ  129 (562)
T 3ghg_A          114 DLRSRIEVLKRKVIEK  129 (562)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4444444444444433

>3m91_A Proteasome-associated ATPase; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis} PDB: 3m9h_A

Probab=84.87  E-value=4.2  Score=28.46  Aligned_cols=40  Identities=30%  Similarity=0.390  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          132 RCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQL  171 (302)
Q Consensus       132 kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkL  171 (302)
                      ++.+++.++..|..+|..|.+.+.+-.-|+.+|.+-.++|
T Consensus        10 r~~~l~~~l~~L~~rN~rL~~~L~~AR~el~~Lkeele~L   49 (51)
T 3m91_A           10 DIHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4566777888888888888888887777777777666665

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=84.33  E-value=15  Score=29.80  Aligned_cols=45  Identities=18%  Similarity=0.363  Sum_probs=23.3

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022126          138 QEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESMKRSA  182 (302)
Q Consensus       138 ~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~~rsa  182 (302)
                      ..+.+|+..+.+|...+.+..+..++...--+.||.+.+.+++..
T Consensus        40 ~~v~ql~~~i~~Le~eL~e~r~~~q~a~~e~e~Lr~e~~~l~~~~   84 (120)
T 3i00_A           40 RVVLQLKGHVSELEADLAEQQHLRQQAADDCEFLRAELDELRRQR   84 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            334444555555555555555444554445556666666554443

>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens}

Probab=84.25  E-value=1.7  Score=30.55  Aligned_cols=25  Identities=12%  Similarity=0.315  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHH
Q 022126          127 QKMAKRCQMMEQEIESLSKDKQELQ  151 (302)
Q Consensus       127 ~kl~~kl~~me~E~e~LrKkn~ELq  151 (302)
                      +.|+..+++++.+.+.|+++++||+
T Consensus        22 eaLk~E~~eLk~k~~~L~~~~~el~   46 (53)
T 2yy0_A           22 ELLRLELAEMKEKYEAIVEENKKLK   46 (53)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333333

>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B*

Probab=84.19  E-value=34  Score=33.81  Aligned_cols=17  Identities=24%  Similarity=0.344  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 022126          160 QKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       160 q~~qLqelYdkLK~~~e  176 (302)
                      .++.|+..++.|+.++.
T Consensus       169 ~i~~L~~~~~~l~~ki~  185 (464)
T 1m1j_B          169 SLRVLRAVIDSLHKKIQ  185 (464)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            34445555555555443

>3vmx_A Voltage-gated hydrogen channel 1; coiled-coil, ION channel, ION transport, membrane protein; 1.45A {Mus musculus}

Probab=83.68  E-value=5.2  Score=27.71  Aligned_cols=38  Identities=11%  Similarity=0.200  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFS  155 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~  155 (302)
                      +++.+...++.|..|+++++..++.+.++++-|+..++
T Consensus         5 ~l~kLKe~n~~L~~kv~~Le~~c~~~eQEieRL~~LLk   42 (48)
T 3vmx_A            5 QILRLKQINIQLATKIQHLEFSCSEKEQEIERLNKLLK   42 (48)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHH
Confidence            33444444445555555665555555555555555544

>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein, LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3 g.39.1.3

Probab=83.03  E-value=0.97  Score=32.62  Aligned_cols=43  Identities=12%  Similarity=0.210  Sum_probs=29.8

Q ss_pred             CccccCcccccCCcEEecCCccccH-HHHHhhhcCCCCCCCCcccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCT-EDANKILSNDAACPICDQVL   45 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~-~Ci~~~~~~~~~CPvC~~~l   45 (302)
                      |.|..|.+.|.+..+...=|.+||. .|..+.+  ...|-.|+..+
T Consensus        28 F~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f--~~~C~~C~~~~   71 (76)
T 1iml_A           28 LKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMF--GPKGFGRGGAE   71 (76)
T ss_dssp             CBCTTTCCBCCTTTEEEETTEEEETTTHHHHHS--SCCCSSCCCSS
T ss_pred             CCccccCccCCCCceECcCCeEeeCHHHHHHHh--CccCCCcCCce
Confidence            5677888888755566667888888 5876653  45677777543

>1wfk_A Zinc finger, FYVE domain containing 19; riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Mus musculus} SCOP: g.50.1.1

Probab=82.88  E-value=0.021  Score=44.27  Aligned_cols=67  Identities=16%  Similarity=0.400  Sum_probs=42.7

Q ss_pred             ccccCcccccC---CcEEecCCccccHHHHHhhh-------cCCCCCCCCccccccCC-CcccccCCChHHHHHHhcC
Q 022126            2 RCNACWRELEG---RAISTTCGHLLCTEDANKIL-------SNDAACPICDQVLSKSL-MKPVDINPNDEWVNMAMAG   68 (302)
Q Consensus         2 ~CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~-------~~~~~CPvC~~~l~~~d-iv~~~LnPse~~Kt~vL~G   68 (302)
                      .|.+|...|+-   .--=-.||++||..|.....       ...+.|-.|-..+.... .-.....|.+.|+..+-+|
T Consensus        11 ~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~~~lp~~g~~~~RVC~~C~~~l~~~~~~~~~~~~pP~~~~~~~~~~   88 (88)
T 1wfk_A           11 RCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILTRGSSDNASKWSPPQNYKSGPSSG   88 (88)
T ss_dssp             BCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHHHHCCCCCCSSSCCCSCCSSSSCCC
T ss_pred             CCcCcCCcccCccccccCCCCCCEEChhHcCCceeccccCCCcCEECHHHHHHHHhcccccccccCCCHHHHhhccCC
Confidence            58899988751   22235699999999987532       23567999988886543 2223335666666554443

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

Probab=82.82  E-value=14  Score=40.08  Aligned_cols=22  Identities=18%  Similarity=0.377  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHH
Q 022126          133 CQMMEQEIESLSKDKQELQEKF  154 (302)
Q Consensus       133 l~~me~E~e~LrKkn~ELq~ky  154 (302)
                      ++.|+.|...|++.+.||....
T Consensus      1025 v~~L~~e~~~L~qq~~~l~~~~ 1046 (1080)
T 2dfs_A         1025 VSELKEQNTLLKTEKEELNRRI 1046 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444333

>3htk_A Structural maintenance of chromosomes protein 5; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=82.68  E-value=9.9  Score=26.43  Aligned_cols=26  Identities=12%  Similarity=0.061  Sum_probs=9.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          147 KQELQEKFSEKSRQKRKLDEMYDQLR  172 (302)
Q Consensus       147 n~ELq~ky~EKsRq~~qLqelYdkLK  172 (302)
                      .++++..|..-...+.++.+-..+++
T Consensus        28 ~~~~k~~~~~~~~~l~~~~~~I~~~k   53 (60)
T 3htk_A           28 FLKAKEKINEIFEKLNTIRDEVIKKK   53 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=82.43  E-value=1.1  Score=35.00  Aligned_cols=46  Identities=20%  Similarity=0.504  Sum_probs=35.3

Q ss_pred             ccccCccccc----CCcE--EecCCccccHHHHHhhhc-CCCCCCCCcccccc
Q 022126            2 RCNACWRELE----GRAI--STTCGHLLCTEDANKILS-NDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~----~~~v--vT~CGHiFC~~Ci~~~~~-~~~~CPvC~~~l~~   47 (302)
                      .|.||...+.    +.++  --.|+--.|..|..-... ....||.|++.+..
T Consensus        18 iCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYkr   70 (93)
T 1weo_A           18 FCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             BCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             ccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCcccc
Confidence            5999999863    2333  345888999999987654 47889999999864

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A

Probab=82.24  E-value=1.4  Score=37.62  Aligned_cols=33  Identities=15%  Similarity=0.419  Sum_probs=28.0

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS   33 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~   33 (302)
                      |.|..|.+.|.+..+...=|.+||..|..+.+.
T Consensus        35 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~   67 (192)
T 1b8t_A           35 FLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYG   67 (192)
T ss_dssp             CBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHS
T ss_pred             CcCcccCCcCCCCeeEecCCEeeChhhhHhhcC
Confidence            679999999986667777899999999998764

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=82.24  E-value=1.5  Score=31.16  Aligned_cols=39  Identities=18%  Similarity=0.379  Sum_probs=23.2

Q ss_pred             ccccCcccccC-CcEEecCCccccHHHHHhhhcCCCCCCCCccccccC
Q 022126            2 RCNACWRELEG-RAISTTCGHLLCTEDANKILSNDAACPICDQVLSKS   48 (302)
Q Consensus         2 ~CNiC~~~l~~-~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~   48 (302)
                      .|..|.+.+.. ..++..=|..|-..|        +.|-.|++.|...
T Consensus         7 ~C~~C~~~I~~~~~~~~a~~~~~H~~C--------F~C~~C~~~L~~~   46 (72)
T 1x61_A            7 GCGGCGEDVVGDGAGVVALDRVFHVGC--------FVCSTCRAQLRGQ   46 (72)
T ss_dssp             CCSSSCSCCCSSSCCEECSSSEECTTT--------CBCSSSCCBCTTS
T ss_pred             CCccCCCccCCCceEEEECCCeEcccC--------CcccccCCcCCcC
Confidence            46677776653 345555566555544        4677777777543

>1jcd_A Major outer membrane lipoprotein; protein folding, coiled coil, helix capping, alanine-zipper, membrane protein; 1.30A {Escherichia coli} SCOP: h.1.16.1 PDB: 1eq7_A 1t8z_A* 2guv_A 2gus_A 1jcc_A 1kfn_A 1kfm_A

Probab=82.15  E-value=9.5  Score=26.75  Aligned_cols=46  Identities=13%  Similarity=0.233  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDE  166 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqe  166 (302)
                      ++.++.+.++.|..|+..|..+...++-   +.+...+|-.|-...|.+
T Consensus         5 ki~~Lss~V~~L~~kVdqLssdV~al~~---~v~~ak~eA~RAN~RlDN   50 (52)
T 1jcd_A            5 KADQASSDAQTANAKADQASNDANAARS---DAQAAKDDAARANQRADN   50 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhhhc
Confidence            5566666677777777777777777776   455777787787776654

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

Probab=81.90  E-value=15  Score=31.69  Aligned_cols=60  Identities=15%  Similarity=0.207  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          117 EKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYE  176 (302)
Q Consensus       117 ~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e  176 (302)
                      +++..+.++-+.|.+.+..|+.++++.|+...--.+...|-..+..-|++-.+.+|.++.
T Consensus        55 ~~~~~L~~~k~~Leke~~~LQa~L~qEr~~r~q~se~~~elq~ri~~L~~El~~~k~~~~  114 (168)
T 3o0z_A           55 ERNRILENSKSQTDKDYYQLQAILEAERRDRGHDSEMIGDLQARITSLQEEVKHLKHNLE  114 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444555555555555555554444444444444445555555555554433

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus}

Probab=81.62  E-value=1.4  Score=37.32  Aligned_cols=46  Identities=20%  Similarity=0.530  Sum_probs=36.2

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSL   49 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~d   49 (302)
                      |.|..|.+.|.+..+ ..=|.+||..|..+.+  ...|..|++.+...+
T Consensus        88 F~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f--~~kC~~C~~~I~~~~  133 (182)
T 2jtn_A           88 LKCSDCHVPLAERCF-SRGESVYCKDDFFKRF--GTKCAACQLGIPPTQ  133 (182)
T ss_dssp             TSCTTTCCCCSSCCE-EETTEEECHHHHHHTT--SCCCTTTCCCCCSSC
T ss_pred             CccCCCCCccCCCce-eECCEeeecCcccccc--ccccccCCCccCCCc
Confidence            678899999976555 4679999999988764  468999999886544

>2efr_A General control protein GCN4 and tropomyosin 1 Al; destabilizing cluster, hydrophobic core, contractIle protein; 1.80A {Saccharomyces cerevisiae} PDB: 2efs_A 2d3e_A

Probab=81.53  E-value=23  Score=29.95  Aligned_cols=38  Identities=18%  Similarity=0.295  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 022126          118 KLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFS  155 (302)
Q Consensus       118 ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~  155 (302)
                      ++.++++.++-+.+++..++.+++.|..+...-+.+|.
T Consensus        85 kLKEAE~RAE~AERsv~kLEk~id~lEd~L~~~Kek~~  122 (155)
T 2efr_A           85 KLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYK  122 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333344444444444443333333333

>3l4q_C Phosphatidylinositol 3-kinase regulatory subunit beta; PI3K, phosphoinositide-3-kinase, influenza virus, NS1; 2.30A {Bos taurus} PDB: 2v1y_B

Probab=81.44  E-value=4.5  Score=34.97  Aligned_cols=40  Identities=20%  Similarity=0.394  Sum_probs=35.4

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          138 QEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYES  177 (302)
Q Consensus       138 ~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~  177 (302)
                      ...|.+-++..|+...|.+|+|++.+|-+.|+++..++..
T Consensus        10 ~~ve~v~~~L~e~h~qy~~ks~~yd~l~e~y~r~sqEiq~   49 (170)
T 3l4q_C           10 DSVEAVGAQLKVYHQQYQDKSREYDQLYEEYTRTSQELQM   49 (170)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Confidence            4568888999999999999999999999999999887653

>1p9i_A Cortexillin I/GCN4 hybrid peptide; coiled-coil, unknown function; 1.17A {Synthetic} SCOP: h.1.10.1

Probab=81.30  E-value=1.3  Score=27.33  Aligned_cols=27  Identities=22%  Similarity=0.261  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 022126          127 QKMAKRCQMMEQEIESLSKDKQELQEK  153 (302)
Q Consensus       127 ~kl~~kl~~me~E~e~LrKkn~ELq~k  153 (302)
                      +++..-+.++++|..+|+.+.+||-.+
T Consensus         2 dqlnallasleaenkqlkakveellak   28 (31)
T 1p9i_A            2 DQLNALLASLEAENKQLKAKVEELLAK   28 (31)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445778889999999999888655

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A

Probab=81.18  E-value=1.2  Score=37.18  Aligned_cols=46  Identities=20%  Similarity=0.530  Sum_probs=36.1

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCccccccCC
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSKSL   49 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~d   49 (302)
                      |.|..|.+.|.+..+ ..=|.+||..|..+.+  ...|..|++.+...+
T Consensus        34 F~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f--~~~C~~C~~~I~~~~   79 (169)
T 2rgt_A           34 LKCSDCHVPLAERCF-SRGESVYCKDDFFKRF--GTKCAACQLGIPPTQ   79 (169)
T ss_dssp             SBCTTTCCBCCSCCE-ESSSCEECHHHHHHHH--SCBCTTTCCBCCTTS
T ss_pred             CccCCCCCcCCCCCc-ccCCeeeecccccccc--cccccccccccCCCc
Confidence            678899999976555 4679999999988765  468999998876544

>3cl3_D NF-kappa-B essential modulator; death effector domain, coiled-coil, coiled coil, cytoplasm, disease mutation, ectodermal dysplasia; 3.20A {Homo sapiens}

Probab=81.15  E-value=4.5  Score=33.47  Aligned_cols=50  Identities=22%  Similarity=0.290  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          122 VHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEYESM  178 (302)
Q Consensus       122 ~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~e~~  178 (302)
                      ...++++|.-.+.+|++++.-.+.+       -.|-.|++.+||-.|++|=..|+..
T Consensus        53 ~~~~~d~L~lQ~esmeaalkmEr~~-------~~eEKrkLAqLQ~AY~~LfqeYd~~  102 (130)
T 3cl3_D           53 HSVQVDQLRMQGQSVEAALRMERQA-------ASEEKRKLAQLQVAYHQLFQEYDNH  102 (130)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445666666667777666655554       3345678999999999999999853

>1deb_A APC protein, adenomatous polyposis coli protein; coiled coil, tumor suppressor, structural protein; 2.40A {Homo sapiens} SCOP: h.1.18.1

Probab=80.98  E-value=11  Score=26.31  Aligned_cols=38  Identities=16%  Similarity=0.391  Sum_probs=29.0

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          138 QEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQLRSEY  175 (302)
Q Consensus       138 ~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdkLK~~~  175 (302)
                      ++.+.|+++|--|.+.+++-+.++.||+.--..+|.=+
T Consensus        10 ~QVe~Lk~ENshLrrEL~dNS~~lskLE~ets~mKevl   47 (54)
T 1deb_A           10 KQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVL   47 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHhhHHHHHHHHhhhhhHHHHH
Confidence            45567777777777789999999999987776666543

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

Probab=80.85  E-value=18  Score=28.19  Aligned_cols=39  Identities=18%  Similarity=0.298  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 022126          117 EKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFS  155 (302)
Q Consensus       117 ~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~  155 (302)
                      ++..+++..++.+..+....+.|+..|.++++-|...+.
T Consensus        23 drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~eld   61 (101)
T 3u1c_A           23 DRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTEDSRD   61 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            455555555555555555666666666666665554444

>4dzo_A Mitotic spindle assembly checkpoint protein MAD1; homodimer, kinetochore, mitosis, spindle checkpoint protein, nucleus, cell cycle; HET: MSE; 1.76A {Homo sapiens}

Probab=80.38  E-value=2.8  Score=34.28  Aligned_cols=34  Identities=26%  Similarity=0.344  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 022126          132 RCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLD  165 (302)
Q Consensus       132 kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLq  165 (302)
                      ++.+|+.++++++|+++-|++.|.+|+.++++.=
T Consensus         5 e~~~l~~qi~~~ekr~~RLKevF~~ks~eFReav   38 (123)
T 4dzo_A            5 EVAELKKQVESAELKNQRLKEVFQTKIQEFRKAC   38 (123)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4677888888888999999999998888777653

>2oto_A M protein; helical coiled coil, fibrinogen-binding, virulence factor, S active protein, toxin; 3.04A {Streptococcus pyogenes serotype M1} PDB: 2xny_M

Probab=80.37  E-value=24  Score=29.26  Aligned_cols=28  Identities=25%  Similarity=0.449  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 022126          127 QKMAKRCQMMEQEIESLSKDKQELQEKF  154 (302)
Q Consensus       127 ~kl~~kl~~me~E~e~LrKkn~ELq~ky  154 (302)
                      ..+..++.+|+...+.|+.++.++...|
T Consensus        53 ~eL~~~~~~Le~~n~~L~~~lke~~~~~   80 (155)
T 2oto_A           53 EELEKAKQALEDQRKDLETKLKELQQDY   80 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333344444444444444444444444

>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B*

Probab=80.24  E-value=16  Score=36.18  Aligned_cols=11  Identities=27%  Similarity=0.456  Sum_probs=6.6

Q ss_pred             CCcCccccCCC
Q 022126          226 DIWPARQNSSN  236 (302)
Q Consensus       226 ~~~~~~~~~~~  236 (302)
                      -||...||...
T Consensus       252 gGWtViQrR~d  262 (464)
T 1m1j_B          252 GGWTLIQNRQD  262 (464)
T ss_dssp             SCEEEEEEESS
T ss_pred             CCeEEEEEeec
Confidence            36766666544

>2efr_A General control protein GCN4 and tropomyosin 1 Al; destabilizing cluster, hydrophobic core, contractIle protein; 1.80A {Saccharomyces cerevisiae} PDB: 2efs_A 2d3e_A

Probab=80.18  E-value=26  Score=29.65  Aligned_cols=64  Identities=16%  Similarity=0.360  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 022126          107 KCEAMQEKFTEKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKRKLDEMYDQ  170 (302)
Q Consensus       107 K~e~L~~~l~~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~qLqelYdk  170 (302)
                      |++.-...|.++|..+...++.+..+....+..+..|.+.+..|-+.+.....++..++.-.|.
T Consensus        67 kasqrEd~yEeqIk~L~~kLKEAE~RAE~AERsv~kLEk~id~lEd~L~~~Kek~~~i~~eLd~  130 (155)
T 2efr_A           67 KYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYKAISEEMKQ  130 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444555555555555555555555555666666666666665555555555555444443

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

Probab=80.13  E-value=19  Score=27.94  Aligned_cols=46  Identities=20%  Similarity=0.397  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 022126          117 EKLEQVHTAYQKMAKRCQMMEQEIESLSKDKQELQEKFSEKSRQKR  162 (302)
Q Consensus       117 ~ki~e~~s~~~kl~~kl~~me~E~e~LrKkn~ELq~ky~EKsRq~~  162 (302)
                      ++..+++..++.+..+....+.++..|+++++-|...+..-.-++.
T Consensus        23 d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~eld~~~e~l~   68 (101)
T 3u59_A           23 DRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEKYSESVK   68 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555566666777777777666655554433333

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	302
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	5e-05

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 38.8 bits (90), Expect = 5e-05
 Identities = 9/46 (19%), Positives = 18/46 (39%)

Query: 2  RCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK 47
          RC  C  +    +++  C H  C     + +  +  CP+C   +  
Sbjct: 7  RCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES 52

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	302
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.32
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.27
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.16
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.14
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.12
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.11
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.1
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.04
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.99
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	98.95
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.91
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	98.85
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.79
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.67
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.62
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.96
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	97.93
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	92.83
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	86.96
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	86.69
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	85.72
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	83.17
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	83.02
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	81.24
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	80.39

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.32  E-value=2.2e-13  Score=96.38  Aligned_cols=52  Identities=13%  Similarity=0.205  Sum_probs=46.9

Q ss_pred             CccccCcccccCCcEEe-cCCccccHHHHHhhhcCCCCCCCCccccccCCCccc
Q 022126            1 MRCNACWRELEGRAIST-TCGHLLCTEDANKILSNDAACPICDQVLSKSLMKPV   53 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT-~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~div~~   53 (302)
                      |.|+||.+.+. +||++ .|||+||.+||.+|+....+||+|+++++.+|++++
T Consensus         1 l~C~Ic~~~~~-~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLipi   53 (56)
T d2baya1           1 MLCAISGKVPR-RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEI   53 (56)
T ss_dssp             CCCTTTCSCCS-SEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEEC
T ss_pred             CCCccCCchHH-hcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhceeC
Confidence            68999999986 68877 699999999999999988899999999999998764

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.27  E-value=1.8e-12  Score=99.66  Aligned_cols=50  Identities=24%  Similarity=0.522  Sum_probs=43.7

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc-CCCCCCCCccccccCCCc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS-NDAACPICDQVLSKSLMK   51 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~-~~~~CPvC~~~l~~~div   51 (302)
                      +.|+||...+. +|++|.|||+||..|+.+|+. ....||.|+.++...++.
T Consensus        24 l~C~IC~~~~~-~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          24 ISCQICEHILA-DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (86)
T ss_dssp             TBCTTTCSBCS-SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             cCCccCCcchh-cceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhcc
Confidence            57999999886 699999999999999999986 567899999998776653

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=9.2e-12  Score=93.65  Aligned_cols=50  Identities=22%  Similarity=0.482  Sum_probs=43.0

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhc-CCCCCCCCccccccCCCcc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILS-NDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~-~~~~CPvC~~~l~~~div~   52 (302)
                      .|+||+..+. +++++.|||+||..|+.+|+. +...||+|++.+...+.+.
T Consensus        25 ~C~IC~~~~~-~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i~   75 (79)
T d1fbva4          25 LCKICAENDK-DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIV   75 (79)
T ss_dssp             BCTTTSSSBC-CEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCCSS
T ss_pred             CCccCCCcCC-CeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCceee
Confidence            5999999885 699999999999999999986 4678999999998755433

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.14  E-value=7.6e-12  Score=97.91  Aligned_cols=50  Identities=26%  Similarity=0.735  Sum_probs=42.8

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC---CCCCCCCccccccCCCc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN---DAACPICDQVLSKSLMK   51 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~---~~~CPvC~~~l~~~div   51 (302)
                      |.|+||...+. +|+++.|||+||..|+.+|+..   ...||+|++.+...++.
T Consensus        22 l~CpIC~~~~~-~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~   74 (103)
T d1jm7a_          22 LECPICLELIK-EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQ   74 (103)
T ss_dssp             TSCSSSCCCCS-SCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCB
T ss_pred             cCCCccCchhC-CeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCC
Confidence            57999999886 6999999999999999999864   35899999998766553

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.12  E-value=1.8e-11  Score=91.24  Aligned_cols=51  Identities=18%  Similarity=0.386  Sum_probs=45.1

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~div~   52 (302)
                      |.|+||...+. +||++.|||+||..|+.+|+.. ...||.|+..++..++++
T Consensus         9 l~CpIc~~~m~-dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~p   60 (78)
T d1t1ha_           9 FRCPISLELMK-DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTP   60 (78)
T ss_dssp             SSCTTTSCCCS-SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEE
T ss_pred             CCCcCcCchhh-CceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcccccc
Confidence            68999999996 6999999999999999999865 678999999998777654

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.11  E-value=1e-11  Score=93.03  Aligned_cols=51  Identities=14%  Similarity=0.183  Sum_probs=44.1

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhc-CCCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILS-NDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~-~~~~CPvC~~~l~~~div~   52 (302)
                      |.|+||...+. +||++.|||+||..||.+++. ....||.|++.++..++++
T Consensus         8 l~CpIc~~l~~-dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~p   59 (80)
T d2c2la2           8 LCGKISFELMR-EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIP   59 (80)
T ss_dssp             TBCTTTCSBCS-SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEE
T ss_pred             ccCcCcCchhh-hhcccCCcCeecHHHHHHHHhcCCccCCCcccccccccccc
Confidence            68999999986 699999999999999999986 4678999999987665543

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.10  E-value=1.1e-11  Score=90.41  Aligned_cols=46  Identities=20%  Similarity=0.627  Sum_probs=41.4

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      .|+||+..+.+.++++.|||+||..|+.+|+.....||+|++.+..
T Consensus         7 ~C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           7 RCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCccCCcCccCCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            5999999997667789999999999999999989999999998753

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.04  E-value=5e-11  Score=86.33  Aligned_cols=49  Identities=27%  Similarity=0.575  Sum_probs=40.5

Q ss_pred             ccccCccccc----CCcEEecCCccccHHHHHhhhcC-CCCCCCCccccccCCC
Q 022126            2 RCNACWRELE----GRAISTTCGHLLCTEDANKILSN-DAACPICDQVLSKSLM   50 (302)
Q Consensus         2 ~CNiC~~~l~----~~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~~di   50 (302)
                      .|+||...+.    ...+++.|||+||..|+.+|+.. ...||+|++.+...++
T Consensus         5 ~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~~   58 (65)
T d1g25a_           5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             CCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccccc
Confidence            6999998653    13578899999999999999864 6689999999977654

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=4.1e-11  Score=92.68  Aligned_cols=47  Identities=21%  Similarity=0.619  Sum_probs=39.1

Q ss_pred             CccccCcccccCCcE-EecCCccccHHHHHhhhcCCCCCCCCccccccCCC
Q 022126            1 MRCNACWRELEGRAI-STTCGHLLCTEDANKILSNDAACPICDQVLSKSLM   50 (302)
Q Consensus         1 l~CNiC~~~l~~~~v-vT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~~di   50 (302)
                      |.|+||...|. +|| ++.|||+||..|+.+|+.  ..||+|+..+...++
T Consensus        23 l~C~IC~~~~~-~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l   70 (97)
T d1jm7b_          23 LRCSRCTNILR-EPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDL   70 (97)
T ss_dssp             TSCSSSCSCCS-SCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSC
T ss_pred             CCCccCCchhh-cCceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhC
Confidence            57999999996 466 468999999999999974  469999998776554

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.95  E-value=1.4e-10  Score=80.49  Aligned_cols=47  Identities=26%  Similarity=0.608  Sum_probs=39.2

Q ss_pred             CccccCcccccC---CcEEecCCccccHHHHHhhhcC-CCCCCCCcccccc
Q 022126            1 MRCNACWRELEG---RAISTTCGHLLCTEDANKILSN-DAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~~~-~~~CPvC~~~l~~   47 (302)
                      |.|+||+..+..   .++++.|||+||..|+.+|+.. ..+||+|++++.+
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            579999998852   3456789999999999999875 5689999998864

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.91  E-value=4e-10  Score=87.84  Aligned_cols=51  Identities=10%  Similarity=0.075  Sum_probs=44.6

Q ss_pred             CccccCcccccCCcEEecCCc-cccHHHHHhhhcCCCCCCCCccccccCCCcc
Q 022126            1 MRCNACWRELEGRAISTTCGH-LLCTEDANKILSNDAACPICDQVLSKSLMKP   52 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGH-iFC~~Ci~~~~~~~~~CPvC~~~l~~~div~   52 (302)
                      |.|+||...|. +||++.||| +||..||.+|+.....||+|+++++..++++
T Consensus        23 f~CPI~~~lm~-dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~p   74 (98)
T d1wgma_          23 FLDPIMSTLMC-DPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRP   74 (98)
T ss_dssp             TBCTTTCSBCS-SEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEE
T ss_pred             hCCcCchhHHH-HHHhcccccchhhHHHHHHHHHhcCCcccccccccchhhcc
Confidence            78999999996 699998765 8999999999988889999999988766654

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.85  E-value=1.7e-10  Score=81.65  Aligned_cols=43  Identities=28%  Similarity=0.594  Sum_probs=37.4

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHhhhcCCCCCCCCcccccc
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANKILSNDAACPICDQVLSK   47 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~~   47 (302)
                      |.|.||.+.+. +++++.|||+||..|+.++   ...||+|++.+..
T Consensus         7 l~C~IC~~~~~-~p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~   49 (56)
T d1bora_           7 LRCQQCQAEAK-CPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPL   49 (56)
T ss_dssp             SSCSSSCSSCB-CCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSC
T ss_pred             CCCcccCcccC-CCEEecCCCHHhHHHHHcC---CCcCcCCCCcccC
Confidence            57999999886 6899999999999998754   6789999998764

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=98.79  E-value=1.2e-09  Score=76.66  Aligned_cols=45  Identities=31%  Similarity=0.698  Sum_probs=37.8

Q ss_pred             CccccCcccccC--CcE-EecCCccccHHHHHhhhcCCCCCCCCcccc
Q 022126            1 MRCNACWRELEG--RAI-STTCGHLLCTEDANKILSNDAACPICDQVL   45 (302)
Q Consensus         1 l~CNiC~~~l~~--~~v-vT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l   45 (302)
                      ..|.||+..+..  ..+ ++.|||+||..|+.+|+.....||+|++.+
T Consensus         6 ~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i   53 (55)
T d1iyma_           6 VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV   53 (55)
T ss_dssp             CCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCS
T ss_pred             CCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEe
Confidence            369999999863  343 347999999999999999999999999865

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.67  E-value=4.4e-09  Score=82.79  Aligned_cols=47  Identities=21%  Similarity=0.441  Sum_probs=37.4

Q ss_pred             ccccCcccccC-----------------CcEEecCCccccHHHHHhhhcC-----CCCCCCCccccccC
Q 022126            2 RCNACWRELEG-----------------RAISTTCGHLLCTEDANKILSN-----DAACPICDQVLSKS   48 (302)
Q Consensus         2 ~CNiC~~~l~~-----------------~~vvT~CGHiFC~~Ci~~~~~~-----~~~CPvC~~~l~~~   48 (302)
                      .|.||...|..                 ...++.|||+||..||..|+..     ..+||+|++.+...
T Consensus        27 ~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          27 DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             EETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            49999998742                 1357889999999999999864     34899999988543

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.62  E-value=1.1e-08  Score=77.68  Aligned_cols=45  Identities=16%  Similarity=0.405  Sum_probs=37.4

Q ss_pred             ccccCcccccC-----------------CcEEecCCccccHHHHHhhhcCCCCCCCCccccc
Q 022126            2 RCNACWRELEG-----------------RAISTTCGHLLCTEDANKILSNDAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~-----------------~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~~l~   46 (302)
                      .|.||+..+..                 ..+++.|||+||..||.+|++...+||+|++.+.
T Consensus        23 ~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          23 NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             CCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             cCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            37788776532                 2567899999999999999998899999999874

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.96  E-value=1.1e-06  Score=66.32  Aligned_cols=43  Identities=19%  Similarity=0.413  Sum_probs=32.4

Q ss_pred             CccccCcccccC-C-cEEecCCccccHHHHHhhhcC--------CCCCCCCcc
Q 022126            1 MRCNACWRELEG-R-AISTTCGHLLCTEDANKILSN--------DAACPICDQ   43 (302)
Q Consensus         1 l~CNiC~~~l~~-~-~vvT~CGHiFC~~Ci~~~~~~--------~~~CPvC~~   43 (302)
                      ..|+||+..+.. + +.++.|||.||..|+..+++.        ...||.|+-
T Consensus         6 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           6 SGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             CCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            369999988752 3 345579999999999998741        236998764

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=97.93  E-value=2.2e-06  Score=60.07  Aligned_cols=44  Identities=25%  Similarity=0.428  Sum_probs=35.3

Q ss_pred             ccccCcccccCCcEEecC-----CccccHHHHHhhhc--CCCCCCCCccccc
Q 022126            2 RCNACWRELEGRAISTTC-----GHLLCTEDANKILS--NDAACPICDQVLS   46 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~C-----GHiFC~~Ci~~~~~--~~~~CPvC~~~l~   46 (302)
                      .|.||+..+.+ ..++.|     +|.|+..|+.+|+.  ...+||+|++.++
T Consensus         8 ~C~IC~~~~~~-~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           8 VCWICNEELGN-ERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             EETTTTEECSC-CCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCccCCccCCC-ceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            59999988753 445554     59999999999985  4678999999875

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=92.83  E-value=0.02  Score=34.33  Aligned_cols=30  Identities=27%  Similarity=0.615  Sum_probs=26.3

Q ss_pred             CccccCcccccCCcEEecCCccccHHHHHh
Q 022126            1 MRCNACWRELEGRAISTTCGHLLCTEDANK   30 (302)
Q Consensus         1 l~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~   30 (302)
                      |+|..|.+.|....+...=|.|||..|..+
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeeec
Confidence            689999999987778888999999999764

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.96  E-value=0.13  Score=30.86  Aligned_cols=29  Identities=21%  Similarity=0.586  Sum_probs=26.4

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHh
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANK   30 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~   30 (302)
                      +|.+|..+|.+..+++.=+.|+|-.|..+
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~sr   29 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTTR   29 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHTT
T ss_pred             CchhhccccccCcccccCCeEeecccccc
Confidence            59999999998899999999999999764

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=86.69  E-value=0.27  Score=36.45  Aligned_cols=46  Identities=20%  Similarity=0.496  Sum_probs=35.8

Q ss_pred             ccccCccccc----CCcEE--ecCCccccHHHHHhhhc-CCCCCCCCcccccc
Q 022126            2 RCNACWRELE----GRAIS--TTCGHLLCTEDANKILS-NDAACPICDQVLSK   47 (302)
Q Consensus         2 ~CNiC~~~l~----~~~vv--T~CGHiFC~~Ci~~~~~-~~~~CPvC~~~l~~   47 (302)
                      .|.||.+.+.    +.++|  ..|+--.|..|..-..+ ....||.|++.+..
T Consensus        18 ~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr   70 (93)
T d1weoa_          18 FCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             BCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             hhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhh
Confidence            5999998763    34444  35899999999987665 47889999999865

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.72  E-value=0.017  Score=38.89  Aligned_cols=42  Identities=14%  Similarity=0.541  Sum_probs=28.0

Q ss_pred             ccccCcccccC---CcEEecCCccccHHHHHhhhcCCCCCCCCcc
Q 022126            2 RCNACWRELEG---RAISTTCGHLLCTEDANKILSNDAACPICDQ   43 (302)
Q Consensus         2 ~CNiC~~~l~~---~~vvT~CGHiFC~~Ci~~~~~~~~~CPvC~~   43 (302)
                      .|.+|...|+-   .--=..||++||..|..+.....+.|..|.+
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~~   46 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQR   46 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHhh
Confidence            48888888752   3334579999999997665444667877765

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.17  E-value=0.43  Score=28.89  Aligned_cols=31  Identities=13%  Similarity=0.291  Sum_probs=27.8

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhh
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKIL   32 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~   32 (302)
                      .|..|..+|..+.+|..=+++||..|..+-|
T Consensus         1 ~C~~C~qPIGtksfipk~~~~yCvpCyE~kf   31 (32)
T d1x4ka1           1 ICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH   31 (32)
T ss_dssp             CCSSSCCCCCSSSEEEETTEEEEHHHHHHHT
T ss_pred             CcccccCcccccccccCCCCceEeecchhhc
Confidence            4899999998899999999999999987653

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.02  E-value=0.39  Score=33.10  Aligned_cols=40  Identities=23%  Similarity=0.619  Sum_probs=28.5

Q ss_pred             ccccCcccccCCcE--EecCCccccHHHHHhhhcCCCCCCCC
Q 022126            2 RCNACWRELEGRAI--STTCGHLLCTEDANKILSNDAACPIC   41 (302)
Q Consensus         2 ~CNiC~~~l~~~~v--vT~CGHiFC~~Ci~~~~~~~~~CPvC   41 (302)
                      .|-.|...|++..+  -..|+++||.+|=.=.-+.-..||-|
T Consensus        17 ~C~gC~~~l~~~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          17 FCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             EETTTTEECTTSEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CccCCCCcCCCCceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            47789888875432  45799999999954433345679987

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.24  E-value=0.59  Score=28.25  Aligned_cols=31  Identities=19%  Similarity=0.396  Sum_probs=27.6

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHhhh
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANKIL   32 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~~~   32 (302)
                      .|+.|..+|..+-+|-.=+|+||..|..+-|
T Consensus         1 ~C~~C~qPIGtkSFip~~~~~yCvpCYE~kf   31 (32)
T d1wyha1           1 LCSGCEQPLGSRSFVPDKGAHYCVPCYENKF   31 (32)
T ss_dssp             BCTTTCCBTTTSCEEEETTEEEEHHHHHHHT
T ss_pred             CcccccCcccccccccCCCcEEEEecccccc
Confidence            4999999998889999999999999987643

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=80.39  E-value=0.31  Score=29.30  Aligned_cols=29  Identities=17%  Similarity=0.472  Sum_probs=25.0

Q ss_pred             ccccCcccccCCcEEecCCccccHHHHHh
Q 022126            2 RCNACWRELEGRAISTTCGHLLCTEDANK   30 (302)
Q Consensus         2 ~CNiC~~~l~~~~vvT~CGHiFC~~Ci~~   30 (302)
                      .|..|++.|....|...=+-|+|+.|.-+
T Consensus         1 lC~~C~K~LdStTva~h~~eiYCKsCygk   29 (32)
T d1a7ia2           1 LCMVCRKNLDSTTVAIHDAEVYCKSCYGK   29 (32)
T ss_dssp             ECSSSCCEECSSCCEEETTEEECSHHHHH
T ss_pred             CchhhhhccCcceeeeecceEEehhhccc
Confidence            49999999987778888899999999765