Psyllid ID: psy10214

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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-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-----
Protein Sequence
MMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPDGRSLSPLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAHQGSTSSASGTTPPNSTPTQSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPDGRR
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccEccccccccccccccccccccHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccc
Coil and Loop (DISEMBL)
mmfmgpggprgggnagpppfpsagpggmggpgnlgpggmgpggllqgplaylekttsniglpdgrslsplekdEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTkedevsttlekDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSalkpelivKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLqgwakspahqgstssasgttppnstptqsgpgisamggplpgmmggmapivpgstmqpmsgmpqqQQQVQMQQQIHMQHMqqqgmgpggppsgpggpssgmmfmgpggprgggnagpppfpsagpggmggpgnlgpggmgpggllqgplaylekttsniglpdgrr
Flexible Loop (DISEMBL)
MMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTTSniglpdgrslspLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEdevsttlekdeiklEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAHQGstssasgttppnstpTQSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLekttsniglpdgrr
Low Complexity Region (SEG)
MMFMgpggprgggnagpppfpsagpggmggpgnlgpggmgpggllqgplAYLEKTTSNIGLPDGRSLSPLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAHQgstssasgttppnstptqsgpgISamggplpgmmggmapIVPGSTmqpmsgmpqqqqqvqmqqqihmqhmqqqgmgpggppsgpggpssgmmfmgpggprgggnagpppfpsagpggmggpgnlgpggmgpggllqgpLAYLEKTTSNIGLPDGRR
Disordered region (IsUnstruct)
************************************************LAYL**********************IKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGW*******************************************************************************************************************************************************************
Disordered Region (DISOPRED)
********************************************LQGPLAYLEKTTSNIGLPDGR*L*PLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIV****M****IVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDE*************I*QATLKFLDLARQMEAFFLQKRFLLSAL**********************LIKRHYDKIAVWQ************************************************************************************************************************************************************YLEKTTS****P****
Disordered Region (DISEMBL)
*************NAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPDGRSLSPLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGW**************************GPGISAMGGPLPGMMGGMAPIVPGSTMQ************************************PGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPDGRR
Disordered Region (DISPRO)
*****************PPFPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPDGRSLSPLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKED*VSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQG***************************************************************************************************************************************************AY**K*TS*********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPDGRSLSPLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAHQGSTSSASGTTPPNSTPTQSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPDGRR
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	415	2.2.26 [Sep-21-2011]
Q17P98	184	Mediator of RNA polymeras	N/A	N/A	0.253	0.570	0.636	3e-34
Q294G7	190	Mediator of RNA polymeras	yes	N/A	0.339	0.742	0.424	4e-24
Q9VBQ9	189	Mediator of RNA polymeras	yes	N/A	0.231	0.507	0.505	2e-22
Q9H204	178	Mediator of RNA polymeras	yes	N/A	0.306	0.713	0.421	4e-21
Q2TBN4	178	Mediator of RNA polymeras	yes	N/A	0.289	0.674	0.428	1e-20
A4IIZ9	169	Mediator of RNA polymeras	yes	N/A	0.262	0.644	0.427	2e-20
P68943	178	Mediator of RNA polymeras	yes	N/A	0.291	0.679	0.417	5e-20
Q920D3	178	Mediator of RNA polymeras	yes	N/A	0.289	0.674	0.420	5e-20
Q5RKN3	179	Mediator of RNA polymeras	yes	N/A	0.257	0.597	0.444	3e-19

>sp|Q17P98|MED28_AEDAE Mediator of RNA polymerase II transcription subunit 28 OS=Aedes aegypti GN=MED28 PE=3 SV=1

 Score =  146 bits (368), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 70/110 (63%), Positives = 91/110 (82%), Gaps = 5/110 (4%)

Query: 149 NLLSDL----QSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFL 204
           NL+ +L    QSC+  LTKE E +T ++KDEIKLE+DQ TLKF+DLARQMEAFFLQKRFL
Sbjct: 10  NLVDELEEAFQSCIHALTKE-ESATGVDKDEIKLEVDQTTLKFIDLARQMEAFFLQKRFL 68

Query: 205 LSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAK 254
           LSALKP+L++KE+  DL+ ++ARK+ELI++HY+KI  W+NLLSD Q + K
Sbjct: 69  LSALKPDLLLKEENFDLKQEIARKDELIRKHYEKIESWKNLLSDQQNYNK 118

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.
Aedes aegypti (taxid: 7159)

>sp|Q294G7|MED28_DROPS Mediator of RNA polymerase II transcription subunit 28 OS=Drosophila pseudoobscura pseudoobscura GN=MED28 PE=3 SV=1

 Score =  112 bits (281), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 65/153 (42%), Positives = 96/153 (62%), Gaps = 12/153 (7%)

Query: 154 LQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELI 213
            QSCL  LTK++  S T  K+EI+LE+ + T +F+D+ARQMEAFFLQKRFL+S LKP ++
Sbjct: 19  FQSCLLSLTKQEPNSGT-NKEEIELEVQKTTNRFIDVARQMEAFFLQKRFLVSTLKPYML 77

Query: 214 VKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKS----PAHQGSTSSASGTT 269
           +K++  DL  ++ RKE L+++HY+++  W+  LSD+Q    +    P + G     SG  
Sbjct: 78  IKDENQDLSIEIQRKEALLQKHYNRLEEWKACLSDIQQGVHNRPTPPINPGMLQGPSGMQ 137

Query: 270 PPNSTPTQSGPGISAMGGPLPGM-MGGMAPIVP 301
            P       G G+    G +PGM  GGM+P+ P
Sbjct: 138 QP------MGGGVPPRPGLMPGMPPGGMSPVGP 164

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

>sp|Q9VBQ9|MED28_DROME Mediator of RNA polymerase II transcription subunit 28 OS=Drosophila melanogaster GN=MED28 PE=1 SV=1

 Score =  107 bits (266), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 49/97 (50%), Positives = 73/97 (75%), Gaps = 1/97 (1%)

Query: 154 LQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELI 213
            QSCL  LTK++  S T  K+EI LE+ + T +F+D+ARQMEAFFLQKRFL+S LKP ++
Sbjct: 19  FQSCLLTLTKQEPNSGT-NKEEIDLEVQKTTNRFIDVARQMEAFFLQKRFLVSTLKPYML 77

Query: 214 VKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQ 250
           +K++  DL  ++ RKE L+++HY+++  W+  LSD+Q
Sbjct: 78  IKDENQDLSIEIQRKEALLQKHYNRLEEWKACLSDIQ 114

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Drosophila melanogaster (taxid: 7227)

>sp|Q9H204|MED28_HUMAN Mediator of RNA polymerase II transcription subunit 28 OS=Homo sapiens GN=MED28 PE=1 SV=1

 Score =  103 bits (256), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 56/133 (42%), Positives = 80/133 (60%), Gaps = 6/133 (4%)

Query: 149 NLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSAL 208
            L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  
Sbjct: 47  ELESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQ 105

Query: 209 KPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAH--QGSTS--- 263
           KPE ++KED+ +LR++L RK+ L+++H  K+  WQ +L D+    K PA   QGS +   
Sbjct: 106 KPEQVIKEDVSELRNELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPADIPQGSLAYLE 165

Query: 264 SASGTTPPNSTPT 276
            AS   P    PT
Sbjct: 166 QASANIPAPLKPT 178

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May be part of a complex containing NF2/merlin that participates in cellular signaling to the actin cytoskeleton downstream of tyrosine kinase signaling pathways.

Homo sapiens (taxid: 9606)

>sp|Q2TBN4|MED28_BOVIN Mediator of RNA polymerase II transcription subunit 28 OS=Bos taurus GN=MED28 PE=2 SV=1

 Score =  101 bits (251), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 54/126 (42%), Positives = 78/126 (61%), Gaps = 6/126 (4%)

Query: 150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
           L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct: 48  LESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIKKFLDIARQTECFFLQKRLQLSVQK 106

Query: 210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAH--QGSTS---S 264
           PE ++KED+ +LR++L RK+ L+++H  K+  WQ +L D+    K PA   QGS +    
Sbjct: 107 PEQVIKEDVSELRNELQRKDALVQKHLTKLRHWQQVLEDINMQHKKPADIPQGSLAYLEQ 166

Query: 265 ASGTTP 270
           AS   P
Sbjct: 167 ASANIP 172

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May be part of a complex containing NF2/merlin that participates in cellular signaling to the actin cytoskeleton downstream of tyrosine kinase signaling pathways.

Bos taurus (taxid: 9913)

>sp|A4IIZ9|MED28_XENTR Mediator of RNA polymerase II transcription subunit 28 OS=Xenopus tropicalis GN=med28 PE=2 SV=1

 Score =  100 bits (248), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 47/110 (42%), Positives = 72/110 (65%), Gaps = 1/110 (0%)

Query: 149 NLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSAL 208
           +L S  ++C   L  +D V+ T +++EI+  ++Q   KFLD+ARQ E FFLQKR  LS  
Sbjct: 38  DLESSFEACFASLVSQDYVNGT-DQEEIRTGVEQCIQKFLDVARQTECFFLQKRLQLSVQ 96

Query: 209 KPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAH 258
           KPE ++KED+ +LR++L RKE LI++H  K+  WQ +L ++ G  K  + 
Sbjct: 97  KPEQVIKEDVSELRNELQRKEALIQKHLTKLRSWQQVLEEINGQHKKTSE 146

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Xenopus tropicalis (taxid: 8364)

>sp|P68943|MED28_RAT Mediator of RNA polymerase II transcription subunit 28 OS=Rattus norvegicus GN=Med28 PE=1 SV=1

 Score = 99.4 bits (246), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 53/127 (41%), Positives = 77/127 (60%), Gaps = 6/127 (4%)

Query: 149 NLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSAL 208
            L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  
Sbjct: 47  ELESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQ 105

Query: 209 KPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAH--QGSTS--- 263
           KP+ ++KED+ +LR +L RK+ L+++H  K+  WQ +L D+    K PA   QGS +   
Sbjct: 106 KPDQVIKEDVSELRSELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPADMPQGSLAYLE 165

Query: 264 SASGTTP 270
            AS   P
Sbjct: 166 QASANIP 172

May be part of a complex containing NF2/merlin that participates in cellular signaling to the actin cytoskeleton downstream of tyrosine kinase signaling pathways (By similarity). Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Rattus norvegicus (taxid: 10116)

>sp|Q920D3|MED28_MOUSE Mediator of RNA polymerase II transcription subunit 28 OS=Mus musculus GN=Med28 PE=2 SV=2

 Score = 99.0 bits (245), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 53/126 (42%), Positives = 77/126 (61%), Gaps = 6/126 (4%)

Query: 150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
           L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct: 48  LESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQK 106

Query: 210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAH--QGSTS---S 264
           P+ ++KED+ +LR +L RK+ L+++H  K+  WQ +L D+    K PA   QGS +    
Sbjct: 107 PDQVIKEDVSELRSELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPADMPQGSLAFLEQ 166

Query: 265 ASGTTP 270
           AS   P
Sbjct: 167 ASANIP 172

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May be part of a complex containing NF2/merlin that participates in cellular signaling to the actin cytoskeleton downstream of tyrosine kinase signaling pathways.

Mus musculus (taxid: 10090)

>sp|Q5RKN3|MED28_DANRE Mediator of RNA polymerase II transcription subunit 28 OS=Danio rerio GN=med28 PE=2 SV=1

 Score = 96.7 bits (239), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 48/108 (44%), Positives = 68/108 (62%), Gaps = 1/108 (0%)

Query: 150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
           L +  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct: 49  LEASFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDVARQTECFFLQKRLQLSVQK 107

Query: 210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPA 257
           PE + KED  +L+++L RKE LI++H  KI  WQ +L D+    K P 
Sbjct: 108 PEQVEKEDASELKNELQRKEMLIQKHLAKIHHWQQVLEDINVQHKKPT 155

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Danio rerio (taxid: 7955)

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	415
350397326	270	PREDICTED: hypothetical protein LOC10074	0.561	0.862	0.483	3e-41
332029089	274	Mediator of RNA polymerase II transcript	0.575	0.872	0.472	1e-40
383847953	266	PREDICTED: uncharacterized protein LOC10	0.539	0.842	0.475	1e-40
189234764	198	PREDICTED: similar to mediator complex [	0.313	0.656	0.6	9e-39
110764402	260	PREDICTED: hypothetical protein LOC72666	0.527	0.842	0.472	4e-38
380024459	200	PREDICTED: mediator of RNA polymerase II	0.253	0.525	0.678	4e-37
307205253	201	Mediator of RNA polymerase II transcript	0.253	0.522	0.657	6e-37
340725940	270	PREDICTED: hypothetical protein LOC10064	0.253	0.388	0.652	1e-36
242021293	275	mediator of RNA polymerase II transcript	0.301	0.454	0.625	6e-36
307185667	266	Mediator of RNA polymerase II transcript	0.253	0.394	0.631	2e-35

>gi|350397326|ref|XP_003484842.1| PREDICTED: hypothetical protein LOC100745114 [Bombus impatiens]

 Score =  176 bits (445), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 135/279 (48%), Positives = 156/279 (55%), Gaps = 46/279 (16%)

Query: 154 LQSCLQVLTKEDE--------VS--TTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRF 203
            Q CL +L  +DE        VS   T++K+E + E++Q TL+F+DLARQMEAFFLQKRF
Sbjct: 19  FQQCLSILITKDEGLGNNGIGVSGGLTVDKEEARSEVEQVTLRFIDLARQMEAFFLQKRF 78

Query: 204 LLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAHQGSTS 263
           LLSALKPEL++KEDI DLR +LARKE+LIKRHYDKI VWQNLL+DLQGWAKSPA QG   
Sbjct: 79  LLSALKPELVIKEDINDLRVELARKEDLIKRHYDKITVWQNLLADLQGWAKSPA-QGP-- 135

Query: 264 SASGTTPPNSTP--TQSGPG-ISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQVQM 320
                  PN  P  TQ+G    SA GG    M       +     Q      Q Q   Q 
Sbjct: 136 ------APNGLPNGTQTGQNQQSANGGGNATMQ--QQQQILQHQQQLQQQQQQLQHLQQH 187

Query: 321 QQQIHMQHMQQQGMGPGGPPSG---PGGPSSGM--MFMGPGGPRGGGNAGPPPFPSAGPG 375
           Q Q    H QQ   G G PP+      G S G   MFM  GG    G  G   FP AG G
Sbjct: 188 QMQQQQLHQQQVQQGSGAPPTSGLQGVGVSVGQQGMFMTQGGVSVTGTRG--GFPVAGVG 245

Query: 376 GMGGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPDGR 414
                             LQGPLA+LEKTTSNIG+P+ R
Sbjct: 246 SSA---------------LQGPLAFLEKTTSNIGMPERR 269

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332029089|gb|EGI69103.1| Mediator of RNA polymerase II transcription subunit 28 [Acromyrmex echinatior]

 Score =  174 bits (440), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 131/277 (47%), Positives = 162/277 (58%), Gaps = 38/277 (13%)

Query: 154 LQSCLQVLTKEDEVST---------TLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFL 204
            Q CL +LTK++ +           T++KDE + EI+QAT++F+DLARQMEA+FLQKRFL
Sbjct: 19  FQQCLSILTKDEGLGNSGTGASGGLTVDKDEGRAEIEQATMRFIDLARQMEAYFLQKRFL 78

Query: 205 LSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAHQGSTSS 264
           LSALKPE++VKE+I +L+ +LARKEELIKRH DKIAVWQN+LSDLQGWA+SPA QG   S
Sbjct: 79  LSALKPEMLVKEEINELKLELARKEELIKRHNDKIAVWQNMLSDLQGWAQSPA-QGPAPS 137

Query: 265 A--SGTTPPNSTPTQSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQVQMQQ 322
              +G     +     G G ++M      +             Q     PQ QQQ+Q Q 
Sbjct: 138 GLPNGNQSGQNQQATGGSGNASMQQQQQILQHQQQLQQQLQQQQQQQQHPQLQQQLQQQM 197

Query: 323 QIHMQHMQQQGMGPGGPPS----GPGGPSSGM-MFMGPGGPRGGGNAGPPPFPSAGPGGM 377
           Q  +Q   QQ  G GGPP+    G G P +   MFM  GG   GG A   P      GGM
Sbjct: 198 QHPLQSQVQQ--GSGGPPTSGLQGVGVPVNQQGMFMTQGGV--GGRATGFPV-----GGM 248

Query: 378 GGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPDGR 414
           G               LQGPLAYLEKTTSNIG+P+ R
Sbjct: 249 GSSA------------LQGPLAYLEKTTSNIGMPERR 273

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847953|ref|XP_003699617.1| PREDICTED: uncharacterized protein LOC100877461 [Megachile rotundata]

 Score =  173 bits (439), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 135/284 (47%), Positives = 156/284 (54%), Gaps = 60/284 (21%)

Query: 154 LQSCLQVLTKEDE------VSTT----LEKDEIKLEIDQATLKFLDLARQMEAFFLQKRF 203
            Q CL +L  +DE      +  T    ++K+E + E++Q TL+F+DLARQMEAFFLQKRF
Sbjct: 19  FQQCLSILITKDEGLGNNGIGVTGGLIVDKEEARSEVEQVTLRFIDLARQMEAFFLQKRF 78

Query: 204 LLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAHQGSTS 263
           LLSALKPEL+VKEDI DLR +LARKE+LIKRHYDKI VWQNLL+DLQGWAKSPA QG   
Sbjct: 79  LLSALKPELVVKEDISDLRVELARKEDLIKRHYDKITVWQNLLADLQGWAKSPA-QGP-- 135

Query: 264 SASGTTPPNSTP--TQSGPGISAMGGPLPGMMGGMAPI----VPGSTMQPMSGMPQQQQQ 317
                  PN  P  TQSG       G      GG A I          Q +    Q Q Q
Sbjct: 136 ------APNGLPNGTQSGQNQQTTNG------GGNATIQQQQQMLQHQQQLQQQQQLQHQ 183

Query: 318 VQMQQQIHMQHMQQQGMGPGGPPSG---PGGPSSGM--MFMGPG--GPRGGGNAGPPPFP 370
           +Q Q Q    H QQ   G G PP+      G S G   MFM  G  G R G       FP
Sbjct: 184 MQHQMQQQQLHQQQVQQGSGAPPTSGLQGVGVSVGQQGMFMTQGVTGARAG-------FP 236

Query: 371 SAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPDGR 414
             G G                  LQGPLA+LEKTTSNIG+P+ R
Sbjct: 237 VGGVGSSA---------------LQGPLAFLEKTTSNIGMPERR 265

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189234764|ref|XP_001815546.1| PREDICTED: similar to mediator complex [Tribolium castaneum] gi|270002198|gb|EEZ98645.1| hypothetical protein TcasGA2_TC001173 [Tribolium castaneum]

 Score =  167 bits (423), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 87/145 (60%), Positives = 110/145 (75%), Gaps = 15/145 (10%)

Query: 154 LQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELI 213
            Q CL VLTKE+ V  + +KDE+K+E++Q TL+F+DLARQMEAFFLQKRFLLSALKPE+I
Sbjct: 19  FQHCLNVLTKEEAVPNS-DKDEMKVEVEQTTLRFIDLARQMEAFFLQKRFLLSALKPEMI 77

Query: 214 VKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAHQGSTSSASGTTPPNS 273
           VKEDI + R +LARK+EL+KRHY+KIAVWQNLL+DLQG+AKSPA QGS           +
Sbjct: 78  VKEDINEYRLELARKDELLKRHYEKIAVWQNLLADLQGYAKSPA-QGS-----------A 125

Query: 274 TPTQSGPGISAMGGPLPGMMGGMAP 298
           TPT +  G  ++  P+ G+ G   P
Sbjct: 126 TPTLNNGG--SVQSPMAGLPGNQTP 148

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110764402|ref|XP_001122387.1| PREDICTED: hypothetical protein LOC726666 [Apis mellifera]

 Score =  165 bits (417), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 130/275 (47%), Positives = 149/275 (54%), Gaps = 56/275 (20%)

Query: 154 LQSCLQVLTKEDE--------VS--TTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRF 203
            Q CL +L  +DE        VS   T++K+E + E++Q TL+F+DLARQMEAFFLQKRF
Sbjct: 19  FQQCLSILITKDEGLGNNGIGVSGGLTVDKEEARSEVEQVTLRFIDLARQMEAFFLQKRF 78

Query: 204 LLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAHQGSTS 263
           LLSALKPEL+VKEDI DLR +LARKE+LIKRHYDKI VWQNLL+DLQGWAKSPA QG   
Sbjct: 79  LLSALKPELVVKEDINDLRVELARKEDLIKRHYDKITVWQNLLADLQGWAKSPA-QGP-- 135

Query: 264 SASGTTPPNSTP--TQSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQVQMQ 321
                  PN  P  TQSG    +  G   G    M         Q +    QQ Q +Q  
Sbjct: 136 ------APNGLPNGTQSGQNQQSANG---GGNTTMQQQQQILQHQQLQQQQQQLQHLQQH 186

Query: 322 QQIHMQHMQQQGMGPGGPP-SGPGGPSSGM----MFMGPG-----GPRGGGNAGPPPFPS 371
           Q     H QQ   G G PP SG  G    +    MFM  G     G R G       FP 
Sbjct: 187 QMQQQLHQQQVQQGSGAPPTSGLQGVGVAVGQQGMFMTQGAVGVTGTRAG-------FPV 239

Query: 372 AGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTTS 406
           AG G                  LQGPLA+LEKTTS
Sbjct: 240 AGVG---------------SSTLQGPLAFLEKTTS 259

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380024459|ref|XP_003696013.1| PREDICTED: mediator of RNA polymerase II transcription subunit 28-like [Apis florea]

 Score =  162 bits (409), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 78/115 (67%), Positives = 92/115 (80%), Gaps = 10/115 (8%)

Query: 154 LQSCLQVLTKEDE--------VS--TTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRF 203
            Q CL +L  +DE        VS   T++K+E + E++Q TL+F+DLARQMEAFFLQKRF
Sbjct: 19  FQQCLSILITKDEGLGNNGIGVSGGLTVDKEEARSEVEQVTLRFIDLARQMEAFFLQKRF 78

Query: 204 LLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAH 258
           LLSALKPEL+VKEDI DLR +LARKE+LIKRHYDKI VWQNLL+DLQGWAKSPA 
Sbjct: 79  LLSALKPELVVKEDINDLRVELARKEDLIKRHYDKITVWQNLLADLQGWAKSPAQ 133

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307205253|gb|EFN83633.1| Mediator of RNA polymerase II transcription subunit 28 [Harpegnathos saltator]

 Score =  161 bits (407), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 75/114 (65%), Positives = 92/114 (80%), Gaps = 9/114 (7%)

Query: 154 LQSCLQVLTKEDEVSTT---------LEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFL 204
            Q CL +LTK++ +S           ++KDE + E++Q TL+F+DLARQMEAFFLQKRFL
Sbjct: 19  FQQCLSILTKDEGLSNNGIGISNGVAVDKDEARTEVEQVTLRFIDLARQMEAFFLQKRFL 78

Query: 205 LSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAH 258
           LSALKPEL+VKEDI DL+ +L RK+ELIKRHYDKIAVWQ+LL+DLQGWAKSPA 
Sbjct: 79  LSALKPELVVKEDINDLKLELGRKDELIKRHYDKIAVWQSLLADLQGWAKSPAQ 132

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340725940|ref|XP_003401322.1| PREDICTED: hypothetical protein LOC100643863 [Bombus terrestris]

 Score =  160 bits (405), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 75/115 (65%), Positives = 92/115 (80%), Gaps = 10/115 (8%)

Query: 154 LQSCLQVLTKEDE--------VS--TTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRF 203
            Q CL +L  +DE        VS   T++K+E + E++Q TL+F+DLARQMEAFFLQKRF
Sbjct: 19  FQQCLSILITKDEGLGNNGIGVSGGLTVDKEEARSEVEQVTLRFIDLARQMEAFFLQKRF 78

Query: 204 LLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAH 258
           LLSALKPEL++KEDI DLR +LARKE+LIK+HY+KI VWQNLL+DLQGWAKSPA 
Sbjct: 79  LLSALKPELVIKEDINDLRVELARKEDLIKKHYEKITVWQNLLADLQGWAKSPAQ 133

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242021293|ref|XP_002431079.1| mediator of RNA polymerase II transcription subunit, putative [Pediculus humanus corporis] gi|212516328|gb|EEB18341.1| mediator of RNA polymerase II transcription subunit, putative [Pediculus humanus corporis]

 Score =  158 bits (399), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 82/131 (62%), Positives = 98/131 (74%), Gaps = 6/131 (4%)

Query: 154 LQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELI 213
            QSCL VLTKE  + T ++KDEI +++D   LKF+DLARQ+EAFFLQKRFLLSALKPE +
Sbjct: 19  FQSCLNVLTKEGALPT-MDKDEISVDVDHTILKFIDLARQLEAFFLQKRFLLSALKPESV 77

Query: 214 VKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDL--QGWAKSPAHQGSTSSASGTTPP 271
           VKEDI DLR +L RK+ELIKRHY+KI+ WQ LL+DL  Q WAKSPA   S +  +GT  P
Sbjct: 78  VKEDINDLRAELNRKDELIKRHYEKISAWQTLLADLQVQSWAKSPAQGSSNTPLAGT--P 135

Query: 272 NSTPTQSGPGI 282
              PT S P I
Sbjct: 136 TGAPT-SSPNI 145

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307185667|gb|EFN71589.1| Mediator of RNA polymerase II transcription subunit 28 [Camponotus floridanus]

 Score =  156 bits (394), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 92/114 (80%), Gaps = 9/114 (7%)

Query: 154 LQSCLQVLTKEDEVST---------TLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFL 204
            Q CL +L K++ + +         T++KDE + E++QAT++F+DLARQMEAFFLQKRFL
Sbjct: 19  FQQCLSMLIKDEGLVSNGTGASGGLTVDKDEGRAEMEQATMRFIDLARQMEAFFLQKRFL 78

Query: 205 LSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAH 258
           LSALKPE++VKEDI +LR +LARKEELIKRH +KI VWQN+LSDLQGWA+SPA 
Sbjct: 79  LSALKPEMVVKEDIQELRMELARKEELIKRHNEKIVVWQNMLSDLQGWAQSPAQ 132

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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	415
UNIPROTKB|F1MNZ6	178	MED28 "Mediator of RNA polymer	0.257	0.601	0.444	1e-23
UNIPROTKB|Q2TBN4	178	MED28 "Mediator of RNA polymer	0.257	0.601	0.444	1e-23
UNIPROTKB|E2RMT8	175	MED28 "Uncharacterized protein	0.257	0.611	0.444	1e-23
UNIPROTKB|H0YAA8	179	MED28 "Mediator of RNA polymer	0.257	0.597	0.444	1e-23
UNIPROTKB|Q9H204	178	MED28 "Mediator of RNA polymer	0.257	0.601	0.444	1e-23
UNIPROTKB|I3LSW2	178	MED28 "Uncharacterized protein	0.257	0.601	0.444	1e-23
RGD|1305875	178	Med28 "mediator complex subuni	0.257	0.601	0.435	3.4e-23
MGI|MGI:1914249	178	Med28 "mediator of RNA polymer	0.257	0.601	0.435	8.8e-23
UNIPROTKB|E1C5V2	178	MED28 "Uncharacterized protein	0.257	0.601	0.444	1.8e-22
UNIPROTKB|Q294G7	190	MED28 "Mediator of RNA polymer	0.228	0.5	0.510	4.3e-22

UNIPROTKB|F1MNZ6 MED28 "Mediator of RNA polymerase II transcription subunit 28" [Bos taurus (taxid:9913)]

 Score = 246 (91.7 bits), Expect = 1.0e-23, Sum P(2) = 1.0e-23
 Identities = 48/108 (44%), Positives = 71/108 (65%)

Query:   150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
             L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct:    48 LESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQK 106

Query:   210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPA 257
             PE ++KED+ +LR++L RK+ L+++H  K+  WQ +L D+    K PA
Sbjct:   107 PEQVIKEDVSELRNELQRKDALVQKHLTKLRHWQQVLEDINMQHKKPA 154

GO:0051151 "negative regulation of smooth muscle cell differentiation" evidence=IEA

GO:0030864 "cortical actin cytoskeleton" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0016592 "mediator complex" evidence=IEA

UNIPROTKB|Q2TBN4 MED28 "Mediator of RNA polymerase II transcription subunit 28" [Bos taurus (taxid:9913)]

 Score = 246 (91.7 bits), Expect = 1.0e-23, Sum P(2) = 1.0e-23
 Identities = 48/108 (44%), Positives = 71/108 (65%)

Query:   150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
             L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct:    48 LESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIKKFLDIARQTECFFLQKRLQLSVQK 106

Query:   210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPA 257
             PE ++KED+ +LR++L RK+ L+++H  K+  WQ +L D+    K PA
Sbjct:   107 PEQVIKEDVSELRNELQRKDALVQKHLTKLRHWQQVLEDINMQHKKPA 154

GO:0016020 "membrane" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003779 "actin binding" evidence=IEA

UNIPROTKB|E2RMT8 MED28 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 246 (91.7 bits), Expect = 1.0e-23, Sum P(2) = 1.0e-23
 Identities = 48/108 (44%), Positives = 71/108 (65%)

Query:   150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
             L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct:    45 LESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQK 103

Query:   210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPA 257
             PE ++KED+ +LR++L RK+ L+++H  K+  WQ +L D+    K PA
Sbjct:   104 PEQVIKEDVSELRNELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPA 151

GO:0051151 "negative regulation of smooth muscle cell differentiation" evidence=IEA

GO:0030864 "cortical actin cytoskeleton" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0016592 "mediator complex" evidence=IEA

UNIPROTKB|H0YAA8 MED28 "Mediator of RNA polymerase II transcription subunit 28" [Homo sapiens (taxid:9606)]

 Score = 246 (91.7 bits), Expect = 1.0e-23, Sum P(2) = 1.0e-23
 Identities = 48/108 (44%), Positives = 71/108 (65%)

Query:   150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
             L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct:    45 LESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQK 103

Query:   210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPA 257
             PE ++KED+ +LR++L RK+ L+++H  K+  WQ +L D+    K PA
Sbjct:   104 PEQVIKEDVSELRNELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPA 151

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q9H204 MED28 "Mediator of RNA polymerase II transcription subunit 28" [Homo sapiens (taxid:9606)]

 Score = 246 (91.7 bits), Expect = 1.0e-23, Sum P(2) = 1.0e-23
 Identities = 48/108 (44%), Positives = 71/108 (65%)

Query:   150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
             L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct:    48 LESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQK 106

Query:   210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPA 257
             PE ++KED+ +LR++L RK+ L+++H  K+  WQ +L D+    K PA
Sbjct:   107 PEQVIKEDVSELRNELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPA 154

GO:0003779 "actin binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0016592 "mediator complex" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0030864 "cortical actin cytoskeleton" evidence=IEA

GO:0051151 "negative regulation of smooth muscle cell differentiation" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|I3LSW2 MED28 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 246 (91.7 bits), Expect = 1.0e-23, Sum P(2) = 1.0e-23
 Identities = 48/108 (44%), Positives = 71/108 (65%)

Query:   150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
             L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct:    48 LESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQK 106

Query:   210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPA 257
             PE ++KED+ +LR++L RK+ L+++H  K+  WQ +L D+    K PA
Sbjct:   107 PEQVIKEDVSELRNELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPA 154

GO:0051151 "negative regulation of smooth muscle cell differentiation" evidence=IEA

GO:0030864 "cortical actin cytoskeleton" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0016592 "mediator complex" evidence=IEA

RGD|1305875 Med28 "mediator complex subunit 28" [Rattus norvegicus (taxid:10116)]

 Score = 241 (89.9 bits), Expect = 3.4e-23, Sum P(2) = 3.4e-23
 Identities = 47/108 (43%), Positives = 70/108 (64%)

Query:   150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
             L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct:    48 LESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQK 106

Query:   210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPA 257
             P+ ++KED+ +LR +L RK+ L+++H  K+  WQ +L D+    K PA
Sbjct:   107 PDQVIKEDVSELRSELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPA 154

GO:0003779 "actin binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005856 "cytoskeleton" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0016020 "membrane" evidence=IEA

GO:0016592 "mediator complex" evidence=IEA;ISO

GO:0019827 "stem cell maintenance" evidence=IEA;ISO

GO:0030864 "cortical actin cytoskeleton" evidence=IEA;ISO

GO:0051151 "negative regulation of smooth muscle cell differentiation" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

MGI|MGI:1914249 Med28 "mediator of RNA polymerase II transcription, subunit 28 homolog (yeast)" [Mus musculus (taxid:10090)]

 Score = 241 (89.9 bits), Expect = 8.8e-23, Sum P(2) = 8.8e-23
 Identities = 47/108 (43%), Positives = 70/108 (64%)

Query:   150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
             L S  ++C   L  +D V+ T +++EI+  +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct:    48 LESSFEACFASLVSQDYVNGT-DQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQK 106

Query:   210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPA 257
             P+ ++KED+ +LR +L RK+ L+++H  K+  WQ +L D+    K PA
Sbjct:   107 PDQVIKEDVSELRSELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPA 154

GO:0003779 "actin binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0016020 "membrane" evidence=IEA

GO:0016592 "mediator complex" evidence=IDA

GO:0019827 "stem cell maintenance" evidence=IMP

GO:0030864 "cortical actin cytoskeleton" evidence=IDA

GO:0051151 "negative regulation of smooth muscle cell differentiation" evidence=IMP

UNIPROTKB|E1C5V2 MED28 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 234 (87.4 bits), Expect = 1.8e-22, Sum P(2) = 1.8e-22
 Identities = 48/108 (44%), Positives = 68/108 (62%)

Query:   150 LLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK 209
             L +  ++C   L  +D V+ T E   + + +DQ   KFLD+ARQ E FFLQKR  LS  K
Sbjct:    48 LEASFEACFASLVSQDYVNGT-EPAVLPVGVDQCIQKFLDVARQTECFFLQKRLQLSVQK 106

Query:   210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPA 257
             PE ++KED+ +LR++L RKE LI++H  K+  WQ +L D+    K PA
Sbjct:   107 PEQVIKEDVSELRNELQRKEALIQKHLSKLRHWQQVLEDISVQHKKPA 154

GO:0016592 "mediator complex" evidence=IEA

GO:0019827 "stem cell maintenance" evidence=IEA

GO:0030864 "cortical actin cytoskeleton" evidence=IEA

GO:0051151 "negative regulation of smooth muscle cell differentiation" evidence=IEA

UNIPROTKB|Q294G7 MED28 "Mediator of RNA polymerase II transcription subunit 28" [Drosophila pseudoobscura pseudoobscura (taxid:46245)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 49/96 (51%), Positives = 74/96 (77%)

Query:   155 QSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIV 214
             QSCL  LTK++  S T  K+EI+LE+ + T +F+D+ARQMEAFFLQKRFL+S LKP +++
Sbjct:    20 QSCLLSLTKQEPNSGT-NKEEIELEVQKTTNRFIDVARQMEAFFLQKRFLVSTLKPYMLI 78

Query:   215 KEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQ 250
             K++  DL  ++ RKE L+++HY+++  W+  LSD+Q
Sbjct:    79 KDENQDLSIEIQRKEALLQKHYNRLEEWKACLSDIQ 114

GO:0001104 "RNA polymerase II transcription cofactor activity" evidence=ISS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0016592 "mediator complex" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9VBQ9	MED28_DROME	No assigned EC number	0.5051	0.2313	0.5079	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	415
pfam11594	106	pfam11594, Med28, Mediator complex subunit 28	2e-31
pfam11594	106	pfam11594, Med28, Mediator complex subunit 28	9e-28
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	3e-05
pfam08690	298	pfam08690, GET2, GET complex subunit GET2	9e-05
cd00176	213	cd00176, SPEC, Spectrin repeats, found in several	2e-04
COG1340	294	COG1340, COG1340, Uncharacterized archaeal coiled-	4e-04
COG1579	239	COG1579, COG1579, Zn-ribbon protein, possibly nucl	4e-04
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	0.001
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	0.001
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	0.001
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1579	239	COG1579, COG1579, Zn-ribbon protein, possibly nucl	0.003
pfam08317	321	pfam08317, Spc7, Spc7 kinetochore protein	0.003
COG5028	861	COG5028, COG5028, Vesicle coat complex COPII, subu	0.004

>gnl|CDD|192780 pfam11594, Med28, Mediator complex subunit 28

 Score =  115 bits (289), Expect = 2e-31
 Identities = 41/99 (41%), Positives = 60/99 (60%), Gaps = 3/99 (3%)

Query: 175 EIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKR 234
           EI+  +DQ + KFLD+ARQ E FFLQKR  LS  KP+  +KE+   L+ ++ RK++L  +
Sbjct: 1   EIRNYVDQLSQKFLDIARQKETFFLQKRNELSVFKPKKTLKEEAQKLKEEMQRKDQLQTK 60

Query: 235 HYDKIAVWQNLLSDLQGWAKSPA---HQGSTSSASGTTP 270
           H  KI  W+NLL+D +   K      ++G    A  +TP
Sbjct: 61  HDSKIDYWENLLTDAEDVYKVRDEVPNEGRQRIAELSTP 99

Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours. Length = 106

>gnl|CDD|192780 pfam11594, Med28, Mediator complex subunit 28

 Score =  105 bits (263), Expect = 9e-28
 Identities = 36/82 (43%), Positives = 52/82 (63%), Gaps = 6/82 (7%)

Query: 74  EIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARK 133
           EI+  +DQ + KFLD+ARQ E FFLQKR  LS  KP+  +KE      +   L+ ++ RK
Sbjct: 1   EIRNYVDQLSQKFLDIARQKETFFLQKRNELSVFKPKKTLKE------EAQKLKEEMQRK 54

Query: 134 EELIKRHYDKIAVWQNLLSDLQ 155
           ++L  +H  KI  W+NLL+D +
Sbjct: 55  DQLQTKHDSKIDYWENLLTDAE 76

Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours. Length = 106

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 46.3 bits (110), Expect = 3e-05
 Identities = 24/131 (18%), Positives = 32/131 (24%), Gaps = 4/131 (3%)

Query: 265 ASGTTPPNSTPTQSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQVQMQQQI 324
             G   P     +       +  P         P        P+    QQ Q   + QQ+
Sbjct: 200 PPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPL----QQPQFPGLSQQM 255

Query: 325 HMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPGNLG 384
                Q        P      P        PG P+G     PPP        +  P    
Sbjct: 256 PPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQ 315

Query: 385 PGGMGPGGLLQ 395
            G      L+Q
Sbjct: 316 RGPQFREQLVQ 326

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|219971 pfam08690, GET2, GET complex subunit GET2

 Score = 43.6 bits (103), Expect = 9e-05
 Identities = 23/121 (19%), Positives = 39/121 (32%), Gaps = 6/121 (4%)

Query: 259 QGSTSSASGTTPPNSTPT-QSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQ 317
           QGS+      +  ++ P   +G   SA     P +   +  I P    +  S       +
Sbjct: 34  QGSSVKLVSKSVLDAKPEDNTGSTTSAHDQSTPEIQDILEAIDP-PKDESESPAENIDPE 92

Query: 318 VQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGGM 377
           V+M QQ+     + Q  G G         ++ +  M      G G     P  +  P   
Sbjct: 93  VEMFQQL----AKMQQQGNGSDNPPADDSTADLFSMLLQMGGGDGPDSESPASAQEPQEA 148

Query: 378 G 378
            
Sbjct: 149 P 149

This family corresponds to the GET complex subunit GET2. The GET complex is involved in the retrieval of ER resident proteins from the Golgi. Length = 298

>gnl|CDD|238103 cd00176, SPEC, Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 40/177 (22%), Positives = 77/177 (43%), Gaps = 25/177 (14%)

Query: 85  KFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKI 144
           +FL  A ++EA+  +K  LLS+      ++ V  + K    L  +LA  EE ++   +++
Sbjct: 4   QFLRDADELEAWLSEKEELLSSTDYGDDLESVEALLKKHEALEAELAAHEERVEAL-NEL 62

Query: 145 AVWQNLLS-------DLQSCLQVLTKE-DEVSTTLEKDEIKLEIDQATLKFLDLARQMEA 196
              + L+        ++Q  L+ L +  +E+    E+   +LE      +F   A  +E 
Sbjct: 63  G--EQLIEEGHPDAEEIQERLEELNQRWEELRELAEERRQRLEEALDLQQFFRDADDLEQ 120

Query: 197 FFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRH---YDKIAVWQNLLSDLQ 250
           +  +K   L++            DL  DL   EEL+K+H    +++   +  L  L 
Sbjct: 121 WLEEKEAALASE-----------DLGKDLESVEELLKKHKELEEELEAHEPRLKSLN 166

Length = 213

>gnl|CDD|224259 COG1340, COG1340, Uncharacterized archaeal coiled-coil protein [Function unknown]

 Score = 42.0 bits (99), Expect = 4e-04
 Identities = 36/189 (19%), Positives = 79/189 (41%), Gaps = 37/189 (19%)

Query: 63  DGRSLSPLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKD 122
           +  +L       ++ EI++                L+K+   S L PE   +E  +V + 
Sbjct: 100 NEFNLGGRSIKSLEREIER----------------LEKKQQTSVLTPE---EERELV-QK 139

Query: 123 IVDLRHDLARKEELIKRH------YDKIAVWQNLLSDLQSCLQVLTKE-----DEVSTTL 171
           I +LR +L   ++ ++ +        +I   +    ++   +Q L  E     +E+    
Sbjct: 140 IKELRKELEDAKKALEENEKLKELKAEIDELKKKAREIHEKIQELANEAQEYHEEMIKLF 199

Query: 172 EK-DEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELI-VKEDIVDLRHDLARKE 229
           E+ DE++ E D+   +F++L+++++    +       L+ EL  +++ I  LR      +
Sbjct: 200 EEADELRKEADELHEEFVELSKKID----ELHEEFRNLQNELRELEKKIKALRAKEKAAK 255

Query: 230 ELIKRHYDK 238
              KR   K
Sbjct: 256 RREKREELK 264

Length = 294

>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

 Score = 41.2 bits (97), Expect = 4e-04
 Identities = 27/115 (23%), Positives = 46/115 (40%), Gaps = 4/115 (3%)

Query: 126 LRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATL 185
           L  +  R E  IK     +   +  L  L   L+ L  E E     +  +++ EI +   
Sbjct: 15  LDLEKDRLEPRIKEIRKALKKAKAELEALNKALEALEIELE-DLENQVSQLESEIQEIRE 73

Query: 186 KFLDLARQMEAFFLQKRFLLSALKPEL-IVKEDIVDLRHDLARKEELIKRHYDKI 239
           +      ++ A   ++     AL  E+ I KE I  L  +LA   E I++   +I
Sbjct: 74  RIKRAEEKLSAVKDEREL--RALNIEIQIAKERINSLEDELAELMEEIEKLEKEI 126

Length = 239

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 40.5 bits (95), Expect = 0.001
 Identities = 29/134 (21%), Positives = 34/134 (25%), Gaps = 7/134 (5%)

Query: 267 GTTPPNSTPTQSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQVQMQQQIHM 326
              P    P    P  +A     P       P  P    + +          Q   Q  +
Sbjct: 173 PQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPL 232

Query: 327 QHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPG---NL 383
                Q   P   P  P G S  M    P  P+       PP P A P     P     L
Sbjct: 233 PPQLPQQPPPLQQPQFP-GLSQQMP---PPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGL 288

Query: 384 GPGGMGPGGLLQGP 397
             G   P    Q P
Sbjct: 289 PQGQNAPLPPPQQP 302

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 26/119 (21%), Positives = 30/119 (25%), Gaps = 1/119 (0%)

Query: 277 QSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQVQMQQQIHMQHMQQQGMGP 336
             G          P M     P   G       G P  QQQ   Q Q  +Q+ QQQ M  
Sbjct: 181 NQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQ 240

Query: 337 GGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQ 395
              P+              G        G    P         P      GM P  + Q
Sbjct: 241 QQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQ-SQLGMLPNQMQQ 298

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 40.8 bits (95), Expect = 0.001
 Identities = 28/111 (25%), Positives = 34/111 (30%), Gaps = 4/111 (3%)

Query: 255 SPAHQGSTSSASGTTPPNSTPTQSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQ 314
                G   +AS      +   Q   G + MG   P  M  +  + PG     M      
Sbjct: 100 MGQQMGGPGTASNLLQSLNVRGQMPMGAAGMG---PHQMSRVGTMQPGGQAGGMMQQSSG 156

Query: 315 QQQVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAG 365
           Q Q Q   Q+  Q  Q QG    G   G  GP         G P   G  G
Sbjct: 157 QPQSQQPNQMGPQQGQAQGQAG-GMNQGQQGPVGQQQPPQMGQPGMPGGGG 206

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 40.0 bits (93), Expect = 0.002
 Identities = 28/150 (18%), Positives = 36/150 (24%), Gaps = 12/150 (8%)

Query: 257 AHQGSTSSASGTTPPNSTPTQSGPGISAMGGPLPGM-MGGMAPIVPGSTMQPMSGMPQQQ 315
           A Q          P      Q+  G    G  +  M  G   P   G  M          
Sbjct: 57  AAQQQVLQGGQGMPDPINALQNLTGQGTRGPQMGPMGPGPGRP--MGQQMGGPGTASNLL 114

Query: 316 QQVQMQQQIHMQH-----MQQQGMGPGGPPSGPGGPSSGMMFMG----PGGPRGGGNAGP 366
           Q + ++ Q+ M        Q   +G   P    GG             P           
Sbjct: 115 QSLNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQ 174

Query: 367 PPFPSAGPGGMGGPGNLGPGGMGPGGLLQG 396
                   G  G  G   P  MG  G+  G
Sbjct: 175 GQAGGMNQGQQGPVGQQQPPQMGQPGMPGG 204

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

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

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 36/209 (17%), Positives = 86/209 (41%), Gaps = 40/209 (19%)

Query: 71  EKDEIKLEIDQATLKFLDLARQ-----MEAFFLQKRFLLSALKPELIVKEVNMVTKDIVD 125
           E +E++ E+++   + L+L  +      E   L++R      + E + + +  + + I  
Sbjct: 275 ELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEA 334

Query: 126 LRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKE-DEVSTTLEKD---------- 174
           L+ +L  +E L++     +A  +    +L+  L  L +E +E+   L ++          
Sbjct: 335 LKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAE 394

Query: 175 ------EIKLEIDQATLKFLDLARQMEAF----------FLQKRFLLSALKPELI----- 213
                 E+K EI+    +   L+ ++E              + +  L  L  EL      
Sbjct: 395 IRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQ 454

Query: 214 ---VKEDIVDLRHDLARKEELIKRHYDKI 239
              +++ + +L  +LA  +E ++R   ++
Sbjct: 455 LEELRDRLKELERELAELQEELQRLEKEL 483

Length = 1163

>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 22/137 (16%), Positives = 51/137 (37%), Gaps = 19/137 (13%)

Query: 71  EKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDL 130
           +  +++ EI +   +      ++ A   ++     AL  E+ + +     + I  L  +L
Sbjct: 60  QVSQLESEIQEIRERIKRAEEKLSAVKDEREL--RALNIEIQIAK-----ERINSLEDEL 112

Query: 131 ARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEV----------STTLEKDEIKLEI 180
           A   E I++   +I   +  L  L+  L       E             + +++E+K ++
Sbjct: 113 AELMEEIEKLEKEIEDLKERLERLEKNLAEAEARLEEEVAEIREEGQELSSKREELKEKL 172

Query: 181 DQATLKFLDLARQMEAF 197
           D   L   +  R  +  
Sbjct: 173 DPELLSEYE--RIRKNK 187

Length = 239

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

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 24/133 (18%), Positives = 48/133 (36%), Gaps = 19/133 (14%)

Query: 120 TKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLE 179
            + +  L+  L    E +KR  + +    NL++ ++  L+                +K E
Sbjct: 142 MQLLEGLKEGLEENLEGMKRDEELLNKDLNLINSIKPKLRKK-----------LQALKEE 190

Query: 180 IDQATLKFLDLARQMEAFFLQKRFLLSALKPELI-VKEDIVDLRHDLARKEELIKRHYDK 238
           I    L+   LA ++      +   L   + EL  +   I + R  L   ++ ++     
Sbjct: 191 IAS--LR--QLADELNLCDPLE---LEKARQELRSLSVKISEKRKQLEELQQELQELTIA 243

Query: 239 IAVWQNLLSDLQG 251
           I    N  S+L  
Sbjct: 244 IEALTNKKSELLE 256

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

>gnl|CDD|227361 COG5028, COG5028, Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]

 Score = 39.0 bits (91), Expect = 0.004
 Identities = 19/92 (20%), Positives = 22/92 (23%), Gaps = 1/92 (1%)

Query: 277 QSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQQVQMQQQIHMQHMQQQGMGP 336
           Q   G ++            A    G    P    P  QQQ + Q       M   G   
Sbjct: 15  QVHTGAASSKKS-ARPHRAYANFSAGQMGMPPYTTPPLQQQSRRQIDQAATAMHNTGANN 73

Query: 337 GGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPP 368
             P        S   F  P G        P P
Sbjct: 74  PAPSVMSPAFQSQQKFSSPYGGSMADGTAPKP 105

Length = 861

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	415
PF11594	106	Med28: Mediator complex subunit 28; InterPro: IPR0	99.94
PF11594	106	Med28: Mediator complex subunit 28; InterPro: IPR0	99.9
KOG1924|consensus	1102		97.83
PF05983	162	Med7: MED7 protein; InterPro: IPR009244 The Mediat	97.02
KOG0570|consensus	223		96.34
KOG2675|consensus	480		96.09
PF08581	79	Tup_N: Tup N-terminal; InterPro: IPR013890 The N-t	94.83
KOG4368|consensus	757		94.5
PHA02562	562	46 endonuclease subunit; Provisional	94.29
PRK11637	428	AmiB activator; Provisional	94.15
KOG3866|consensus	442		94.07
KOG1924|consensus	1102		93.47
cd00176	213	SPEC Spectrin repeats, found in several proteins i	93.28
PF04652	380	DUF605: Vta1 like; InterPro: IPR006745 This family	93.25
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	93.18
KOG4674|consensus	1822		92.9
KOG0964|consensus	1200		92.76
KOG3091|consensus	508		92.34
PRK09039	343	hypothetical protein; Validated	92.18
PF03904	230	DUF334: Domain of unknown function (DUF334); Inter	91.96
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	91.96
PRK11637	428	AmiB activator; Provisional	91.84
PF06637	442	PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 Th	91.08
PF15469	182	Sec5: Exocyst complex component Sec5	91.02
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	90.91
KOG2391|consensus	365		90.67
KOG1883|consensus	1517		90.62
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	90.41
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	90.25
KOG0977|consensus	546		89.95
PTZ00186	657	heat shock 70 kDa precursor protein; Provisional	89.83
KOG0993|consensus	542		89.53
PF13779	820	DUF4175: Domain of unknown function (DUF4175)	89.53
PF01213	312	CAP_N: Adenylate cyclase associated (CAP) N termin	89.52
KOG0996|consensus	1293		89.43
PF07083	215	DUF1351: Protein of unknown function (DUF1351); In	89.39
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	89.38
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	89.22
PRK04863	1486	mukB cell division protein MukB; Provisional	89.08
KOG0995|consensus	581		88.79
KOG4368|consensus	757		88.67
PTZ00009	653	heat shock 70 kDa protein; Provisional	88.64
KOG3227|consensus	231		88.62
PRK05771	646	V-type ATP synthase subunit I; Validated	88.56
KOG4302|consensus	660		88.45
PF12128	1201	DUF3584: Protein of unknown function (DUF3584); In	88.43
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	88.39
cd07639	200	BAR_ACAP1 The Bin/Amphiphysin/Rvs (BAR) domain of	88.3
PF15290	305	Syntaphilin: Golgi-localised syntaxin-1-binding cl	88.21
cd07637	200	BAR_ACAP3 The Bin/Amphiphysin/Rvs (BAR) domain of	87.65
PF12128	1201	DUF3584: Protein of unknown function (DUF3584); In	87.47
PRK05560	805	DNA gyrase subunit A; Validated	87.38
KOG0999|consensus	772		87.23
cd07638	200	BAR_ACAP2 The Bin/Amphiphysin/Rvs (BAR) domain of	86.51
cd07603	200	BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of	86.33
PF05600	507	DUF773: Protein of unknown function (DUF773); Inte	85.89
PF11867	335	DUF3387: Domain of unknown function (DUF3387); Int	85.77
KOG4274|consensus	742		85.61
PF07739	118	TipAS: TipAS antibiotic-recognition domain; InterP	85.48
PF07989	75	Microtub_assoc: Microtubule associated; InterPro:	85.2
KOG4592|consensus	728		84.9
PF12252	1439	SidE: Dot/Icm substrate protein; InterPro: IPR0210	84.83
cd00890	129	Prefoldin Prefoldin is a hexameric molecular chape	84.65
cd00187	445	TOP4c DNA Topoisomerase, subtype IIA; domain A'; b	84.4
PF05427	361	FIBP: Acidic fibroblast growth factor binding (FIB	84.16
KOG1854|consensus	657		84.11
KOG2129|consensus	552		83.95
PF13514	1111	AAA_27: AAA domain	83.81
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	83.67
KOG0964|consensus	1200		83.66
PF07426	174	Dynactin_p22: Dynactin subunit p22; InterPro: IPR0	83.59
KOG0250|consensus	1074		83.54
PRK10350	145	hypothetical protein; Provisional	83.52
PF04108	412	APG17: Autophagy protein Apg17 ; InterPro: IPR0072	83.51
PF11657	144	Activator-TraM: Transcriptional activator TraM	83.48
PF06248	593	Zw10: Centromere/kinetochore Zw10; InterPro: IPR00	83.4
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	83.33
cd00632	105	Prefoldin_beta Prefoldin beta; Prefoldin is a hexa	83.29
TIGR01061	738	parC_Gpos DNA topoisomerase IV, A subunit, Gram-po	83.28
PF09731	582	Mitofilin: Mitochondrial inner membrane protein; I	83.28
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	83.21
PF09602	165	PhaP_Bmeg: Polyhydroxyalkanoic acid inclusion prot	83.08
PHA02592	439	52 DNA topisomerase II medium subunit; Provisional	82.97
KOG4552|consensus	272		82.97
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	82.95
PF11221	144	Med21: Subunit 21 of Mediator complex; InterPro: I	82.13
KOG0977|consensus	546		82.05
KOG0963|consensus	629		81.7
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	81.63
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	81.59
PF01920	106	Prefoldin_2: Prefoldin subunit; InterPro: IPR00277	81.53
PRK12758	869	DNA topoisomerase IV subunit A; Provisional	81.03
PF00521	426	DNA_topoisoIV: DNA gyrase/topoisomerase IV, subuni	81.02
COG3937	108	Uncharacterized conserved protein [Function unknow	80.38
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	80.33
cd07666	243	BAR_SNX7 The Bin/Amphiphysin/Rvs (BAR) domain of S	80.17

>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]

Probab=99.94  E-value=6.9e-27  Score=199.59  Aligned_cols=78  Identities=56%  Similarity=0.914  Sum_probs=75.8

Q ss_pred             hHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHh
Q psy10214         74 EIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSD  153 (415)
Q Consensus        74 E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsd  153 (415)
                      |||++||++|+||||+|||||+||||||++||++|||++|||      |+.+||.|++||++||+|||+||+.|++++++
T Consensus         1 eirt~vEq~~~~FlD~aRq~e~~FlqKr~~LS~~kpe~~lkE------Ei~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~d   74 (106)
T PF11594_consen    1 EIRTYVEQLIQSFLDVARQMEAFFLQKRFELSAYKPEQVLKE------EINELKEELQRKEQLLQKHYEKIDYWEKLLSD   74 (106)
T ss_pred             CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            799999999999999999999999999999999999999999      99999999999999999999999999999988


Q ss_pred             HHHH
Q psy10214        154 LQSC  157 (415)
Q Consensus       154 fQsc  157 (415)
                      +++.
T Consensus        75 ~~~~   78 (106)
T PF11594_consen   75 AQNQ   78 (106)
T ss_pred             HHhh
Confidence            8764

It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].

>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]

Probab=99.90  E-value=2.3e-23  Score=178.00  Aligned_cols=86  Identities=53%  Similarity=0.849  Sum_probs=83.3

Q ss_pred             hHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Q psy10214        175 EIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAK  254 (415)
Q Consensus       175 EIKv~VEq~tnRFLD~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~~~~  254 (415)
                      |+++.||+++++|||+||++|+|||+|++.+|++||+.++|+||++||.|++||++|++||++||++|+++|+|++++++
T Consensus         1 eirt~vEq~~~~FlD~aRq~e~~FlqKr~~LS~~kpe~~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~d~~~~~k   80 (106)
T PF11594_consen    1 EIRTYVEQLIQSFLDVARQMEAFFLQKRFELSAYKPEQVLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLSDAQNQHK   80 (106)
T ss_pred             CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q psy10214        255 SPAHQG  260 (415)
Q Consensus       255 spaq~~  260 (415)
                      .|++.+
T Consensus        81 ~~~evp   86 (106)
T PF11594_consen   81 VPDEVP   86 (106)
T ss_pred             Cchhcc
Confidence            888864

It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].

>KOG1924|consensus

Probab=97.83  E-value=0.0031  Score=70.10  Aligned_cols=40  Identities=23%  Similarity=0.385  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhcccCCCCCCCCCCCCCCCCCCCCCCCC
Q psy10214        232 IKRHYDKIAVWQNLLSDLQGWAKSPAHQGSTSSASGTTPPNSTPTQ  277 (415)
Q Consensus       232 IqKh~eKIeeWQsvL~dlq~~~~spaq~~~~~~~~~~~~p~~~~~~  277 (415)
                      ++||-+||..-+....    .++||++-+|-  ..++|+|.++|+.
T Consensus       497 l~k~e~Ki~~l~ae~~----al~s~~~~~~~--~~~iP~PP~~pp~  536 (1102)
T KOG1924|consen  497 LQKHEEKIKLLEAEKQ----ALSSPSQLLPI--DGGIPPPPPLPPT  536 (1102)
T ss_pred             HHHhhhhcccCchhhh----hccCcccCCCC--CCCCCCCCCCCCC
Confidence            4444455544433332    46677775443  3455556566553

>PF05983 Med7: MED7 protein; InterPro: IPR009244 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=97.02  E-value=0.0082  Score=54.91  Aligned_cols=56  Identities=18%  Similarity=0.271  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        192 RQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLS  247 (415)
Q Consensus       192 RQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~  247 (415)
                      ..+...|+|.+++++.++|+++...-|..|+.++++|.+.+++..+.++..+++|+
T Consensus       107 ~~i~~L~~NmhhllNeyRPhQARetLi~~me~Ql~~kr~~i~~i~~~~~~~~~~le  162 (162)
T PF05983_consen  107 EDIRLLFINMHHLLNEYRPHQARETLIMMMEEQLEEKREEIEEIRKVCEKAREVLE  162 (162)
T ss_dssp             HHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            57888999999999999999999999999999999999999999999999988874

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 family consists of several eukaryotic proteins, which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multistep process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3FBI_C 3FBN_A 1YKH_A 1YKE_A.

>KOG0570|consensus

Probab=96.34  E-value=0.056  Score=52.25  Aligned_cols=59  Identities=10%  Similarity=0.300  Sum_probs=53.8

Q ss_pred             HHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy10214        193 QMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       193 QLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~  251 (415)
                      .+...|++.+|+++.++|+++..+-|--++.+|+++...++..+..+++-..+|+|...
T Consensus       110 di~tifvnlHHLiNeyRPhQaResLi~lmE~Qi~~~~~~ve~~kk~~~~~~e~l~d~~~  168 (223)
T KOG0570|consen  110 DIRTIFVNLHHLINEYRPHQARESLIMLMERQIEQRSDIVEDFKKHLRQVREVLDDQFQ  168 (223)
T ss_pred             HHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46678999999999999999999999999999999999999999999999999987744

>KOG2675|consensus

Probab=96.09  E-value=0.18  Score=53.43  Aligned_cols=131  Identities=19%  Similarity=0.262  Sum_probs=70.9

Q ss_pred             hHHHHHHHHHHHHHHH------------HHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHh---hh
Q psy10214         78 EIDQATLKFLDLARQM------------EAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRH---YD  142 (415)
Q Consensus        78 ~veq~~~kFid~Arq~------------E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkh---y~  142 (415)
                      -+...+.+|+++++.+            ++||++|-|+.++.+-..=         +..++..=|..-++.|.+.   .+
T Consensus        56 ~i~~~l~~~~~lS~kIggdv~~~~~~v~~~F~s~R~~L~~A~q~qKP---------ds~elad~LkPI~e~i~eI~~fkE  126 (480)
T KOG2675|consen   56 LISEPLAEYLKLSKKIGGDVADVAEMVKSAFASQRAFLWVASQKQKP---------DSNELADLLKPINEEIGEINNFKE  126 (480)
T ss_pred             HHHhHHHHHHHHHHHhChhHHHHHHHHHHHHHHHHHHHHHHHhccCC---------ChHHHHHHhhhHHHhhhHHhhhhh
Confidence            3667788888887754            6899998888776543211         3333443344444333332   22


Q ss_pred             ---HHHHHHHhHHhHHHHhhhh--hcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhhccCchhhhHHH
Q psy10214        143 ---KIAVWQNLLSDLQSCLQVL--TKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKED  217 (415)
Q Consensus       143 ---KIavWqnLlsdfQscLs~L--SkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFLQKrlllSa~KPe~vvKEE  217 (415)
                         +...| |-|+++-.-+..|  ++.+                .+=--|++.++++-.|+.++.+           |  
T Consensus       127 ~nRkS~~F-NhLsav~e~i~algWVav~----------------~tP~p~vke~~daa~FY~NrvL-----------k--  176 (480)
T KOG2675|consen  127 KNRKSPFF-NHLSAVSESIPALGWVAVK----------------PTPAPYVKEFKDAAQFYTNRVL-----------K--  176 (480)
T ss_pred             cccCchHH-HHHHHHHhhcccceeEecC----------------CCCchHHHHHHHHHHHHHHHHH-----------H--
Confidence               34455 4444444444444  2211                2223455666777778888753           2  


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        218 IVDLRHDLARKEELIKRHYDKIAVWQNLLSDL  249 (415)
Q Consensus       218 I~dLK~ELqRKErLIqKh~eKIeeWQsvL~dl  249 (415)
                        ++|..-.+.=+|.+.+++-..+-++-+++-
T Consensus       177 --Eyk~~D~~hveWvKa~l~l~~eL~~YVk~h  206 (480)
T KOG2675|consen  177 --EYKEKDPRHVEWVKAYLALFLELQAYVKEH  206 (480)
T ss_pred             --HhccCChhHHHHHHHHHHHHHHHHHHHHHh
Confidence              344445555566666665555544444444

>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=94.83  E-value=0.054  Score=44.94  Aligned_cols=76  Identities=20%  Similarity=0.288  Sum_probs=54.9

Q ss_pred             HHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHH
Q psy10214        148 QNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLAR  227 (415)
Q Consensus       148 qnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqR  227 (415)
                      .+|++++...|..++.+..++.. ..+|++..|...+    .....+..-++  .+..++.|.++-+.+||..|+.||+.
T Consensus         3 ~elLd~ir~Ef~~~~~e~~~~k~-~~~e~e~ki~~Qi----~Em~~ir~~v~--eLE~~h~kmK~~YEeEI~rLr~eLe~   75 (79)
T PF08581_consen    3 NELLDAIRQEFENLSQEANSYKH-QKDEYEHKINSQI----QEMQQIRQKVY--ELEQAHRKMKQQYEEEIARLRRELEQ   75 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH----HHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-hHHHHHHHHHHHH----HHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46788899999888776655344 5677766665555    55555666666  44566677788889999999999988


Q ss_pred             HHH
Q psy10214        228 KEE  230 (415)
Q Consensus       228 KEr  230 (415)
                      ++.
T Consensus        76 r~~   78 (79)
T PF08581_consen   76 RGR   78 (79)
T ss_dssp             HTT
T ss_pred             hCC
Confidence            753

; PDB: 3VP9_B 3VP8_B.

>KOG4368|consensus

Probab=94.50  E-value=5.5  Score=44.19  Aligned_cols=25  Identities=20%  Similarity=0.415  Sum_probs=16.1

Q ss_pred             hhhHhHhHHHHHHHHHHHHH-HHHHH
Q psy10214         72 KDEIKLEIDQATLKFLDLAR-QMEAF   96 (415)
Q Consensus        72 k~E~~~~veq~~~kFid~Ar-q~E~f   96 (415)
                      +.-|++.|++-|+|.|+-.. -||.|
T Consensus        81 ~~a~~~~~~~~~~k~l~~~~l~~~~~  106 (757)
T KOG4368|consen   81 TAAVAHAVEQQMQKLLEETQLDMNEF  106 (757)
T ss_pred             HHHHHHHHHHHHHHHHHhccCCHHHH
Confidence            34567777888888876543 25555

>PHA02562 46 endonuclease subunit; Provisional

Probab=94.29  E-value=5.1  Score=41.49  Aligned_cols=42  Identities=12%  Similarity=0.275  Sum_probs=19.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhh
Q psy10214        120 TKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVL  161 (415)
Q Consensus       120 ~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~L  161 (415)
                      ++++.++++++...++.|++-.+.+...+.-++.++..+..+
T Consensus       240 ~~~i~~l~~~i~~~~~~L~~l~~~~~~~~~~l~~~~~~~~~~  281 (562)
T PHA02562        240 TDELLNLVMDIEDPSAALNKLNTAAAKIKSKIEQFQKVIKMY  281 (562)
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            333333333333333444444445555555555555554444

>PRK11637 AmiB activator; Provisional

Probab=94.15  E-value=7.8  Score=39.76  Aligned_cols=70  Identities=9%  Similarity=0.084  Sum_probs=29.8

Q ss_pred             hhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhH
Q psy10214         72 KDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDK  143 (415)
Q Consensus        72 k~E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~K  143 (415)
                      .++++..+++.-.+.-++-+++..-.-+  +.-...+-+.+-++.|....+|.++..++.++++.|.+.-.+
T Consensus        49 l~~l~~qi~~~~~~i~~~~~~~~~~~~~--l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~  118 (428)
T PRK11637         49 LKSIQQDIAAKEKSVRQQQQQRASLLAQ--LKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQ  118 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455566655555555444444432221  211112223333334444444444444444444444444333

>KOG3866|consensus

Probab=94.07  E-value=2.3  Score=44.17  Aligned_cols=124  Identities=20%  Similarity=0.314  Sum_probs=73.3

Q ss_pred             HHHHHHHHHHHHHHHhhh------------HHHHHH------------------------------HhHHhHHHHhhhh-
Q psy10214        125 DLRHDLARKEELIKRHYD------------KIAVWQ------------------------------NLLSDLQSCLQVL-  161 (415)
Q Consensus       125 eLR~ElaRKnaLLrkhy~------------KIavWq------------------------------nLlsdfQscLs~L-  161 (415)
                      ++|.+.++-++-++||.+            --+||.                              +|++-|+-.|.-. 
T Consensus       199 ~Rkeaesk~EE~~krH~~HpKvnhPGSkdQLkEVWEE~DgLdpn~fdPKTFF~LHD~NsDGfldeqELEaLFtkELEKvY  278 (442)
T KOG3866|consen  199 ERKEAESKHEESLKRHNDHPKVNHPGSKDQLKEVWEESDGLDPNQFDPKTFFALHDLNSDGFLDEQELEALFTKELEKVY  278 (442)
T ss_pred             HHHHHHHHHHHHHHhhccCccCCCCCcHHHHHHHHHHhcCCCcccCCcchheeeeccCCcccccHHHHHHHHHHHHHHhc
Confidence            555556666788888887            357887                              4555555555432 


Q ss_pred             -hcccccccccchhhHhHhHHHHHHHHHHHHH----HHHHHHHHHHHhhhccCc---------hh-hhHHHHHHHHHHHH
Q psy10214        162 -TKEDEVSTTLEKDEIKLEIDQATLKFLDLAR----QMEAFFLQKRFLLSALKP---------EL-IVKEDIVDLRHDLA  226 (415)
Q Consensus       162 -SkqE~ser~~DqdEIKv~VEq~tnRFLD~AR----QLE~FFLQKrlllSa~KP---------e~-vvKEEI~dLK~ELq  226 (415)
                       .++++. .|.+-+|-...|.-+|++=+|..+    .||.|.- .--.-...-|         +. .+.+|+..+++|++
T Consensus       279 dpkNeeD-DM~EmeEErlRMREHVMk~vDtNqDRlvtleEFL~-~t~~kef~~p~e~WEtl~q~~~yTeEEL~~fE~e~A  356 (442)
T KOG3866|consen  279 DPKNEED-DMKEMEEERLRMREHVMKQVDTNQDRLVTLEEFLN-DTDNKEFNPPKEEWETLGQKKVYTEEELQQFEREYA  356 (442)
T ss_pred             CCCCcch-HHHHHHHHHHHHHHHHHHhcccchhhhhhHHHHHh-hhhhcccCCcchhhhhhcccccccHHHHHHHHHHHH
Confidence             333332 344555555666667777666553    4555443 1111111112         22 45889999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Q psy10214        227 RKEELIKRHYDKIAVWQNLLSDLQ  250 (415)
Q Consensus       227 RKErLIqKh~eKIeeWQsvL~dlq  250 (415)
                      .|++-+.+--+.+..=...|+..+
T Consensus       357 ~ke~El~~ka~~lqq~~ealqr~h  380 (442)
T KOG3866|consen  357 QKEQELQHKAEALQQPPEALQRVH  380 (442)
T ss_pred             HHHHHHhchHHHhhCCHHHHHHHH
Confidence            999888776666655555554444

>KOG1924|consensus

Probab=93.47  E-value=2.4  Score=48.38  Aligned_cols=37  Identities=38%  Similarity=0.752  Sum_probs=21.2

Q ss_pred             CCCCCCCCCC-CCCCCCccCCCCCCCCCCCCCCCCCCC
Q psy10214        266 SGTTPPNSTP-TQSGPGISAMGGPLPGMMGGMAPIVPG  302 (415)
Q Consensus       266 ~~~~~p~~~~-~~~~~~~~~~~g~~~~~~~~map~qq~  302 (415)
                      .++|||.+.| -.+|.+..--++|+||++||-+||.+.
T Consensus       539 ~g~pppPppPPlpggag~PPPPpplPg~aG~PPpPppp  576 (1102)
T KOG1924|consen  539 TGPPPPPPPPPLPGGAGPPPPPPPLPGIAGGPPPPPPP  576 (1102)
T ss_pred             CCCCCCCCCCCCCCCCCCCccCCCCCcccCCCCccCCC
Confidence            3444444443 234455556667788888776665544

>cd00176 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here

Probab=93.28  E-value=4.8  Score=34.48  Aligned_cols=26  Identities=35%  Similarity=0.428  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcC
Q psy10214         83 TLKFLDLARQMEAFFLQKRFLLSALK  108 (415)
Q Consensus        83 ~~kFid~Arq~E~fFLqkr~~ls~~k  108 (415)
                      ..+|.+.++.+++|+-...-.|....
T Consensus         2 ~~~f~~~~~~l~~Wl~~~e~~l~~~~   27 (213)
T cd00176           2 LQQFLRDADELEAWLSEKEELLSSTD   27 (213)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHhcCcc
Confidence            35788888888888887766665443

>PF04652 DUF605: Vta1 like; InterPro: IPR006745 This family contains proteins from the Eukaryota; functionally they are uncharacterised

Probab=93.25  E-value=2.8  Score=41.79  Aligned_cols=83  Identities=16%  Similarity=0.171  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHHHH------HHHHHHHHHhhcChhHHHHhhhhch----hHHHHHHHHHHHHHHHHHHhhhHHHHHHHh
Q psy10214         81 QATLKFLDLARQMEA------FFLQKRFLLSALKPELIVKEVNMVT----KDIVDLRHDLARKEELIKRHYDKIAVWQNL  150 (415)
Q Consensus        81 q~~~kFid~Arq~E~------fFLqkr~~ls~~kpe~i~ke~n~~~----~di~eLR~ElaRKnaLLrkhy~KIavWqnL  150 (415)
                      +.|.+||..|.++|.      ||.+.-++...++-..-.+|...|.    +++++.|+++...++++.+.-.+..|.+=-
T Consensus         1 k~i~~~l~~a~e~~~~~p~v~Y~c~~ya~~~~l~~~~~~~e~~~~~~~Ll~~lE~~K~~~~~~~~~~~~~~~~~~v~~fa   80 (380)
T PF04652_consen    1 KSISPFLKRAQELEKRDPVVAYYCRLYAVEQILKLKLRSKECRQFLTSLLDKLEKMKAELGDNEAILDDVAAQAYVENFA   80 (380)
T ss_dssp             --HHHHHHHHHHHHHCTHHHHHHHHHHHHHHHTT-TT--HHHHHHHHHHHHHHHHHHHCT---CHHC-HHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHhhcCCEEhHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHhhhccCcHHhhcCHHHHHHHHHHHH
Confidence            357899999999994      5655544444444333333322222    244445555554445554444455555544


Q ss_pred             HHhHHHHhhhhhc
Q psy10214        151 LSDLQSCLQVLTK  163 (415)
Q Consensus       151 lsdfQscLs~LSk  163 (415)
                      +.-|..|...+.+
T Consensus        81 ~~~f~~a~~~~~~   93 (380)
T PF04652_consen   81 LKLFNRADKEDRA   93 (380)
T ss_dssp             HHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHc
Confidence            7777777777644

; PDB: 2RKK_B 2RKL_B 3MHV_A.

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

Probab=93.18  E-value=6.4  Score=35.62  Aligned_cols=34  Identities=32%  Similarity=0.517  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        215 KEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSD  248 (415)
Q Consensus       215 KEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~d  248 (415)
                      ++++.+++.++.+.........+++.+-+.+++.
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~  190 (191)
T PF04156_consen  157 REEVQELRSQLERLQENLQQLEEKIQELQELLEQ  190 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4556666666666655566666666666655543

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 [].

>KOG4674|consensus

Probab=92.90  E-value=1.5  Score=53.28  Aligned_cols=118  Identities=27%  Similarity=0.276  Sum_probs=81.6

Q ss_pred             HHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHH-
Q psy10214        113 VKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLA-  191 (415)
Q Consensus       113 ~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~A-  191 (415)
                      +.+.|.+++...-||+|..+....|++-+++|+....=+.-||+.+..|.+.-.. -..+-.-++..+++...||=|.. 
T Consensus      1221 v~~vNll~EsN~~LRee~~~~~~k~qEl~~~i~kl~~el~plq~~l~el~~e~~~-~~ael~~l~~e~~~wK~R~q~L~~ 1299 (1822)
T KOG4674|consen 1221 VEEVNLLRESNKVLREENEANLEKIQELRDKIEKLNFELAPLQNELKELKAELQE-KVAELKKLEEENDRWKQRNQDLLE 1299 (1822)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3457777888899999999999999999998888877777788777776443111 11122233444455554554433 


Q ss_pred             --HHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        192 --RQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQ  243 (415)
Q Consensus       192 --RQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQ  243 (415)
                        +..+--||.+            ++.+|..|+.||..|+++|+.+..++.+-+
T Consensus      1300 k~k~~d~~~~~k------------L~~ei~~Lk~el~~ke~~~~el~~~~~~~q 1341 (1822)
T KOG4674|consen 1300 KYKDSDKNDYEK------------LKSEISRLKEELEEKENLIAELKKELNRLQ 1341 (1822)
T ss_pred             HhhcCCHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              2333334422            256999999999999999999999998877

>KOG0964|consensus

Probab=92.76  E-value=4  Score=47.38  Aligned_cols=78  Identities=15%  Similarity=0.215  Sum_probs=61.4

Q ss_pred             hhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHH
Q psy10214         73 DEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLS  152 (415)
Q Consensus        73 ~E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLls  152 (415)
                      +++-..|+|+++..-.+--+.++||.+.+         .+..|.|+.+++...+...+.-|...|......++...+-.+
T Consensus       695 ~~~~~~i~q~~~~~qk~e~~~~~~~~~~~---------~l~~e~~~~k~e~~~v~~s~~~k~~~Le~i~~~l~~~~~~~~  765 (1200)
T KOG0964|consen  695 EDIDQKIDQLNNNMQKVENDRNAFKREHE---------KLKRELNTIKGEKSRVQESLEPKGKELEEIKTSLHKLESQSN  765 (1200)
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHH---------HHHHHHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence            45667788888888888888888887764         445678888889999999999999988888888877776666


Q ss_pred             hHHHHhh
Q psy10214        153 DLQSCLQ  159 (415)
Q Consensus       153 dfQscLs  159 (415)
                      .|.+.+.
T Consensus       766 ~~e~el~  772 (1200)
T KOG0964|consen  766 YFESELG  772 (1200)
T ss_pred             hHHHHHh
Confidence            6665444

>KOG3091|consensus

Probab=92.34  E-value=5  Score=43.38  Aligned_cols=108  Identities=19%  Similarity=0.192  Sum_probs=52.0

Q ss_pred             HHHHHHHhHHhHH-HHhhhhhcccccc---cccch--hhHhHhHHHHHHHHHHH---HHHHHHHHHHHHHhhhccCc---
Q psy10214        143 KIAVWQNLLSDLQ-SCLQVLTKEDEVS---TTLEK--DEIKLEIDQATLKFLDL---ARQMEAFFLQKRFLLSALKP---  210 (415)
Q Consensus       143 KIavWqnLlsdfQ-scLs~LSkqE~se---r~~Dq--dEIKv~VEq~tnRFLD~---ARQLE~FFLQKrlllSa~KP---  210 (415)
                      ||+..++=+-+|. .+|+.+.+.|-+.   ..+.+  +++.+..+-.+...-+.   -..++.+|=+.|..-++++-   
T Consensus       377 KI~~~k~r~~~Ls~RiLRv~ikqeilr~~G~~L~~~EE~Lr~Kldtll~~ln~Pnq~k~Rl~~L~e~~r~q~~~~~~~~~  456 (508)
T KOG3091|consen  377 KIEEAKNRHVELSHRILRVMIKQEILRKRGYALTPDEEELRAKLDTLLAQLNAPNQLKARLDELYEILRMQNSQLKLQES  456 (508)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcCCccHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHhhcchhccccc
Confidence            8888888888887 6677767766331   23333  34444333211111111   12444444444444334332   


Q ss_pred             ----hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHh
Q psy10214        211 ----ELIVKEDIVDLRHDLARKEELIKRHYDKIAVW-QNLLSDLQ  250 (415)
Q Consensus       211 ----e~vvKEEI~dLK~ELqRKErLIqKh~eKIeeW-QsvL~dlq  250 (415)
                          ++...+....|..|.++...|+.-+++..+.- ..+.++++
T Consensus       457 ~~iD~~~~~e~~e~lt~~~e~l~~Lv~Ilk~d~edi~~~l~E~~~  501 (508)
T KOG3091|consen  457 YWIDFDKLIEMKEHLTQEQEALTKLVNILKGDQEDIKHQLIEDLE  501 (508)
T ss_pred             eeechhhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhHH
Confidence                22323333455555555555555555444444 44445554

>PRK09039 hypothetical protein; Validated

Probab=92.18  E-value=5.5  Score=40.45  Aligned_cols=46  Identities=20%  Similarity=0.256  Sum_probs=26.2

Q ss_pred             hhhccCchh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        204 LLSALKPEL-IVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDL  249 (415)
Q Consensus       204 llSa~KPe~-vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dl  249 (415)
                      .++...|+. .++.+|..|+.+|+.-+..|.-..++.++-+.-++++
T Consensus       131 ~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L  177 (343)
T PRK09039        131 VSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADL  177 (343)
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444 4566777777777666666665555555544444444

>PF03904 DUF334: Domain of unknown function (DUF334); InterPro: IPR005602 This is a family of proteins found in Staphylococcus aureus plasmid with no characterised function

Probab=91.96  E-value=8.3  Score=38.10  Aligned_cols=75  Identities=19%  Similarity=0.257  Sum_probs=50.3

Q ss_pred             chhhHhHhHHHHHHHHHHHHHHHHHHHHH-HHHhhhccCchh---hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        172 EKDEIKLEIDQATLKFLDLARQMEAFFLQ-KRFLLSALKPEL---IVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLL  246 (415)
Q Consensus       172 DqdEIKv~VEq~tnRFLD~ARQLE~FFLQ-KrlllSa~KPe~---vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL  246 (415)
                      +.++++..++.++-+|++.+-.+-.=|+. .+..+..++-+.   ++.+||.+++.|+++.-+=++..+++.+.|++.+
T Consensus        72 ~~~~I~ssL~eTtkdf~~~~~k~~~dF~~~Lq~~Lk~V~tde~k~~~~~ei~k~r~e~~~ml~evK~~~E~y~k~~k~~  150 (230)
T PF03904_consen   72 NLKEIKSSLEETTKDFIDKTEKVHNDFQDILQDELKDVDTDELKNIAQNEIKKVREENKSMLQEVKQSHEKYQKRQKSM  150 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46677777787788888877777666652 233444444443   5577899999888777666777667766666554

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

Probab=91.96  E-value=22  Score=41.32  Aligned_cols=9  Identities=11%  Similarity=0.608  Sum_probs=3.2

Q ss_pred             HHHHHHHHH
Q psy10214        218 IVDLRHDLA  226 (415)
Q Consensus       218 I~dLK~ELq  226 (415)
                      +..++.+++
T Consensus       399 l~~l~~~i~  407 (1163)
T COG1196         399 LEELKREIE  407 (1163)
T ss_pred             HHHHHHHHH
Confidence            333333333

>PRK11637 AmiB activator; Provisional

Probab=91.84  E-value=17  Score=37.35  Aligned_cols=8  Identities=25%  Similarity=0.247  Sum_probs=3.9

Q ss_pred             CCccccCC
Q psy10214        348 SGMMFMGP  355 (415)
Q Consensus       348 ~~~~~~~~  355 (415)
                      +.|+.+..
T Consensus       329 ~~Gi~i~~  336 (428)
T PRK11637        329 WKGMVIGA  336 (428)
T ss_pred             CCCEEeec
Confidence            44555543

>PF06637 PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 This family consists of several PV-1 (PLVAP) proteins, which seem to be specific to mammals

Probab=91.08  E-value=18  Score=38.41  Aligned_cols=58  Identities=17%  Similarity=0.181  Sum_probs=40.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCCCCCCCCCCCCCCCC
Q psy10214        212 LIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQGWAKSPAHQGSTSSASGTTPPN  272 (415)
Q Consensus       212 ~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~~~~spaq~~~~~~~~~~~~p~  272 (415)
                      .+++.|-+.|..||+.|++-++.....++.=-+.|+.--. +|  +|++.|.+-+.-|+||
T Consensus       352 aaLrkerd~L~keLeekkreleql~~q~~v~~saLdtCik-aK--sq~~~p~~r~~~p~pn  409 (442)
T PF06637_consen  352 AALRKERDSLAKELEEKKRELEQLKMQLAVKTSALDTCIK-AK--SQPMTPGPRPVGPVPN  409 (442)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH-hc--cCCCCCCCCCCCCCCC
Confidence            3668889999999999999999888888888887776532 33  4555454444334443

PV-1 is a novel protein component of the endothelial fenestral and stomatal diaphragms []. The function of this family is unknown.

>PF15469 Sec5: Exocyst complex component Sec5

Probab=91.02  E-value=12  Score=33.92  Aligned_cols=84  Identities=7%  Similarity=0.118  Sum_probs=49.1

Q ss_pred             hhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHH---H
Q psy10214         73 DEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQ---N  149 (415)
Q Consensus        73 ~E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWq---n  149 (415)
                      ++++.=|+....+||+|-..++..+-+-+-..+....+..+.+   +.+-+.+.......+-.-|-+...|+....   +
T Consensus         2 ~~lk~LV~~Nf~~Fv~~k~tid~i~~~~~~~~~~~~~~~~~~~---L~~~l~~~~~~~~~~~~pll~~~~k~~~l~~~l~   78 (182)
T PF15469_consen    2 EDLKSLVKENFDKFVSCKDTIDDIYEEFRNMKTEAQQDSGTEK---LEESLNEASSKANSVFKPLLERREKADKLRNALE   78 (182)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhhcccccccHHH---HHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHH
Confidence            5788899999999999999999988776655443222223322   233445555555444444444444444433   4


Q ss_pred             hHHhHHHHhh
Q psy10214        150 LLSDLQSCLQ  159 (415)
Q Consensus       150 LlsdfQscLs  159 (415)
                      ++..++-+|.
T Consensus        79 ~l~r~~flF~   88 (182)
T PF15469_consen   79 FLQRNRFLFN   88 (182)
T ss_pred             HHHHHHHHHH
Confidence            4444444443

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

Probab=90.91  E-value=31  Score=40.18  Aligned_cols=67  Identities=19%  Similarity=0.331  Sum_probs=37.0

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHH
Q psy10214         77 LEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKI  144 (415)
Q Consensus        77 ~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KI  144 (415)
                      .+|+.-+.++=.-|..-+. |+.....+..+.-..++.+|+.+.+++.+++.++.+.++.+.....++
T Consensus       196 ~el~~~l~~L~~q~~~a~~-y~~l~~e~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~  262 (1163)
T COG1196         196 EELEKQLEKLERQAEKAER-YQELKAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQEEL  262 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344333343333333333 333344445555666677777777777777777777766665555533

>KOG2391|consensus

Probab=90.67  E-value=24  Score=36.96  Aligned_cols=66  Identities=18%  Similarity=0.075  Sum_probs=42.9

Q ss_pred             HhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc-ChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q psy10214         75 IKLEIDQATLKFLDLARQMEAFFLQKRFLLSAL-KPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQ  148 (415)
Q Consensus        75 ~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~-kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWq  148 (415)
                      ||++|-.++..=++.+++-|.==++  .+++.+ .-|..|++      ...+|+.|+.+.+.-+..-...|.+..
T Consensus       207 irasvisa~~eklR~r~eeeme~~~--aeq~slkRt~EeL~~------G~~kL~~~~etLEqq~~~L~~niDIL~  273 (365)
T KOG2391|consen  207 IRASVISAVREKLRRRREEEMERLQ--AEQESLKRTEEELNI------GKQKLVAMKETLEQQLQSLQKNIDILK  273 (365)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHhhHHHHHh------hHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence            8888888888877777765543333  233333 34677777      888888888888855555444444433

>KOG1883|consensus

Probab=90.62  E-value=1.7  Score=50.91  Aligned_cols=27  Identities=33%  Similarity=0.254  Sum_probs=17.6

Q ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHhhh
Q psy10214        304 TMQPMSGMPQQQQQVQMQQQIHMQHMQ  330 (415)
Q Consensus       304 ~~q~~~~~~qq~qq~q~q~~~~~q~~~  330 (415)
                      |||.+++++++|||++.+.||||||+.
T Consensus      1430 q~q~t~q~q~~Qqq~~~~~qqqlqhq~ 1456 (1517)
T KOG1883|consen 1430 QMQDTSQHQTIQQQSNHPTQQQLQHQI 1456 (1517)
T ss_pred             hhhhhhHHHHHHHHhcchHHHHHHHhc
Confidence            455556666666666666777777765

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=90.41  E-value=34  Score=38.20  Aligned_cols=37  Identities=11%  Similarity=0.169  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy10214        215 KEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       215 KEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~  251 (415)
                      +.++.++..+++..+.-+....++++.++.-++.++.
T Consensus       874 ~~~~~~l~~~l~~l~~~~~~l~~~~~~l~~~~~~l~~  910 (1164)
T TIGR02169       874 EAALRDLESRLGDLKKERDELEAQLRELERKIEELEA  910 (1164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555555555555555566666655543

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

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

Probab=90.25  E-value=14  Score=36.96  Aligned_cols=37  Identities=16%  Similarity=0.275  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy10214        215 KEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       215 KEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~  251 (415)
                      +.++.+++.++++++.-|+...+++.+...-+++++.
T Consensus       229 k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~  265 (325)
T PF08317_consen  229 KKELAELQEELEELEEKIEELEEQKQELLAEIAEAEK  265 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555555555555555555555555555543

>KOG0977|consensus

Probab=89.95  E-value=30  Score=38.04  Aligned_cols=63  Identities=13%  Similarity=0.157  Sum_probs=35.2

Q ss_pred             hHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-----hhHHHHhhhhchhHHHHHHHHHHHHHHHHH
Q psy10214         76 KLEIDQATLKFLDLARQMEAFFLQKRFLLSALK-----PELIVKEVNMVTKDIVDLRHDLARKEELIK  138 (415)
Q Consensus        76 ~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~k-----pe~i~ke~n~~~~di~eLR~ElaRKnaLLr  138 (415)
                      +.+|+..-.+|.+..+-...+=.+.+-.++.++     -.++.-....+.+|+.+||+|..|..+-|.
T Consensus       119 ~~e~~elr~~~~~~~k~~~~~re~~~~~~~~l~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~  186 (546)
T KOG0977|consen  119 REELKELRKKLEKAEKERRGAREKLDDYLSRLSELEAEINTLKRRIKALEDELKRLKAENSRLREELA  186 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Confidence            345555566666666666555555553333322     123333445566777888888877774433

>PTZ00186 heat shock 70 kDa precursor protein; Provisional

Probab=89.83  E-value=2.4  Score=46.48  Aligned_cols=61  Identities=7%  Similarity=0.078  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHh
Q psy10214        188 LDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKR-------HYDKIAVWQNLLSDLQ  250 (415)
Q Consensus       188 LD~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqK-------h~eKIeeWQsvL~dlq  250 (415)
                      ++.....|.+....+-.+...  ..+..++..+++..+++-++||..       +.+++++-+..+..+.
T Consensus       553 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~  620 (657)
T PTZ00186        553 VEVRNNAETQLTTAERQLGEW--KYVSDAEKENVKTLVAELRKAMENPNVAKDDLAAATDKLQKAVMECG  620 (657)
T ss_pred             HHHHHHHHHHHHHHHHHhhhh--ccCCHHHHHHHHHHHHHHHHHHhcCCcCHHHHHHHHHHHHHHHHHHH
Confidence            344445555555444333221  234455566666666666666653       2334444445555443

>KOG0993|consensus

Probab=89.53  E-value=18  Score=39.05  Aligned_cols=52  Identities=27%  Similarity=0.243  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHHHhhcChhHHHHhhhh----chhHHHHHHHHHHHHHHHHHHhh
Q psy10214         89 LARQMEAFFLQKRFLLSALKPELIVKEVNM----VTKDIVDLRHDLARKEELIKRHY  141 (415)
Q Consensus        89 ~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~----~~~di~eLR~ElaRKnaLLrkhy  141 (415)
                      .+.++|+=|.+||-.+-.-|-|.+-.+ |-    -++|+..||.+|..-.+.....+
T Consensus         3 a~~~l~~e~nqkrk~~~~a~ee~~~rq-~a~~qa~q~dl~~lrtql~~a~aeme~ik   58 (542)
T KOG0993|consen    3 AQQQLEQEFNQKRKELYLAKEEDLKRQ-NAVLQAAQDDLGHLRTQLWEAQAEMENIK   58 (542)
T ss_pred             chhhhhHHHHHhhhhcccchhhHHHhc-cchhhhhcchHHHHHHHHHHHHHHHHHHH
Confidence            578999999999988877777666555 43    36788899999887765554433

>PF13779 DUF4175: Domain of unknown function (DUF4175)

Probab=89.53  E-value=44  Score=38.26  Aligned_cols=127  Identities=14%  Similarity=0.210  Sum_probs=64.5

Q ss_pred             hhchhHHHHHHHHHHHHHHHHHHhhh---HHHHHHHhHHhHHHHhhhhhccc---cccc--ccchhhH----hHhHHHHH
Q psy10214        117 NMVTKDIVDLRHDLARKEELIKRHYD---KIAVWQNLLSDLQSCLQVLTKED---EVST--TLEKDEI----KLEIDQAT  184 (415)
Q Consensus       117 n~~~~di~eLR~ElaRKnaLLrkhy~---KIavWqnLlsdfQscLs~LSkqE---~ser--~~DqdEI----Kv~VEq~t  184 (415)
                      ..+++-..+||..-.|..+.|++.-.   --.+.++|.++++.-+..|..+.   ....  ..+....    ..++++-+
T Consensus       465 G~ls~A~~~Lr~AQe~L~eAL~~gAs~eEI~rLm~eLR~A~~~ym~~LAeq~~~~~~~~~~p~~~~~~~~~~~~dL~~mm  544 (820)
T PF13779_consen  465 GDLSDAERRLRAAQEALREALERGASDEEIARLMQELREAMQDYMQALAEQAQRNPQQQDQPPDQGNSQMMSQQDLQRMM  544 (820)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHhHhCcccccCcccchhhhccCHHHHHHHH
Confidence            44555666777777777777776544   23456677777777777764331   1100  0011111    11133333


Q ss_pred             HHHHHHHH---------HHH---HHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy10214        185 LKFLDLAR---------QME---AFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQ  250 (415)
Q Consensus       185 nRFLD~AR---------QLE---~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq  250 (415)
                      ++.-+.++         .|+   .-.=+.+.    -+++.   ..-.+.+..++....+|++..+-+++--+.+++..
T Consensus       545 d~ie~la~~G~~~~A~q~L~qlq~mmenmq~----~~~q~---~~~~~~~q~m~~L~dl~r~Qq~L~D~tfr~~q~q~  615 (820)
T PF13779_consen  545 DRIEELARSGRMDEARQLLEQLQQMMENMQN----AQPQQ---QQQQEMQQAMEELGDLLRRQQQLMDETFRQLQEQQ  615 (820)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHhccc----cCCCc---hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Confidence            33333331         222   11111111    12232   34556667777777888887777777666666654

>PF01213 CAP_N: Adenylate cyclase associated (CAP) N terminal; InterPro: IPR013992 Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals

Probab=89.52  E-value=1.9  Score=43.73  Aligned_cols=104  Identities=18%  Similarity=0.355  Sum_probs=53.2

Q ss_pred             hHhHHHHHHHHHHHHHHH------------HHHHHHHHHHHhh---cChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHh
Q psy10214         76 KLEIDQATLKFLDLARQM------------EAFFLQKRFLLSA---LKPELIVKEVNMVTKDIVDLRHDLARKEELIKRH  140 (415)
Q Consensus        76 ~~~veq~~~kFid~Arq~------------E~fFLqkr~~ls~---~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkh  140 (415)
                      ..-|+..+.+|+++++.+            ++|-.||+|++.+   .||++-         ++.+          ||+--
T Consensus        50 D~~i~~~l~~f~~~S~~igg~V~~~a~~v~~aF~~qr~~L~~as~~kKP~~~---------~~~~----------lL~Pl  110 (312)
T PF01213_consen   50 DELINGPLKPFVELSKKIGGDVAEQAQLVKKAFQAQRKFLLVASKCKKPDQS---------ELQE----------LLKPL  110 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHBE---HH---------HHHH----------HCHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHccCCCChh---------hHHH----------HHHHH
Confidence            334788899999988765            5788888887754   455332         2222          33333


Q ss_pred             hhHHHHHHHhHHhHH--HHhhhhhcc-cccccccchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        141 YDKIAVWQNLLSDLQ--SCLQVLTKE-DEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRF  203 (415)
Q Consensus       141 y~KIavWqnLlsdfQ--scLs~LSkq-E~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFLQKrl  203 (415)
                      .++|....++.+.=.  .+|+.|++- |.+ .+.-    =+.|+.+=-.|++.++..-.||.||.+
T Consensus       111 ~~~i~~i~~~ke~nR~s~~fNHLsavsEgi-~aLg----WV~v~p~P~~~V~e~~dsA~Fy~NRVL  171 (312)
T PF01213_consen  111 SEAIQKIQEFKEKNRGSKFFNHLSAVSEGI-PALG----WVAVEPKPAPYVKEMKDSAQFYTNRVL  171 (312)
T ss_dssp             HHHHHHHHHHHHTTTTSTTHHHHHHHHCGG-GGGG----GGG--S-HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCchHHHHHHHHHhh-heee----eeeeCCchHhHHHHHHHHHHHHHhHHH
Confidence            333333333333321  133444333 222 2221    111233445677888888889998854

CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [, , , ]. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly [, ]. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity. All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin. CAPs bind G-actin. In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In Saccharomyces cerevisiae (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. S. cerevisiae CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In Schizosaccharomyces pombe (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the S cerevisiae and S. pombe N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase []. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin []. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed. This entry represents the N-terminal domain of CAP proteins. This domain has an all-alpha structure consisting of six helices in a bundle with a left-handed twist and an up-and-down topology [].; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1TJF_B 1S0P_A.

>KOG0996|consensus

Probab=89.43  E-value=17  Score=43.07  Aligned_cols=30  Identities=17%  Similarity=0.134  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy10214        221 LRHDLARKEELIKRHYDKIAVWQNLLSDLQ  250 (415)
Q Consensus       221 LK~ELqRKErLIqKh~eKIeeWQsvL~dlq  250 (415)
                      ++..++.....+..+..+|..|...++.+.
T Consensus      1017 ~~~K~e~~~~~l~e~~~~~~~~~k~~~~l~ 1046 (1293)
T KOG0996|consen 1017 IENKLEAINGELNEIESKIKQPEKELKKLS 1046 (1293)
T ss_pred             HHHHHHHHHHHHHHHHhhhhhHHHhhCccc
Confidence            445566666666677777777776666654

>PF07083 DUF1351: Protein of unknown function (DUF1351); InterPro: IPR009785 This entry is represented by Lactobacillus prophage Lj928, Orf309

Probab=89.39  E-value=20  Score=34.17  Aligned_cols=65  Identities=22%  Similarity=0.368  Sum_probs=41.3

Q ss_pred             CCCCchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhh-HHH
Q psy10214         67 LSPLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYD-KIA  145 (415)
Q Consensus        67 ~~~~~k~E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~-KIa  145 (415)
                      |...+-|+++..|+..+.+|-++.                 --|.-+++.=.++.++.++++.|..++.-|++.|. ++.
T Consensus        12 I~~~n~e~lk~~v~~~~~~Y~~~v-----------------vTee~ik~aKk~rA~LNKl~k~id~~RK~ikk~~~~P~~   74 (215)
T PF07083_consen   12 IEIFNFEELKAEVDEAVEKYKGYV-----------------VTEENIKDAKKDRAELNKLKKAIDDKRKEIKKEYSKPIK   74 (215)
T ss_pred             eecCCHHHHHHHHHHHHHHhCCcc-----------------cChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHH
Confidence            444789999999998888774432                 12333444444566666677777777777777776 354


Q ss_pred             HHH
Q psy10214        146 VWQ  148 (415)
Q Consensus       146 vWq  148 (415)
                      .+.
T Consensus        75 ~Fe   77 (215)
T PF07083_consen   75 EFE   77 (215)
T ss_pred             HHH
Confidence            444

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial and phage proteins of around 230 residues in length. The function of this family is unknown.

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=89.38  E-value=39  Score=37.43  Aligned_cols=16  Identities=6%  Similarity=0.048  Sum_probs=7.6

Q ss_pred             HHHHHHHHHHHHHHHH
Q psy10214         83 TLKFLDLARQMEAFFL   98 (415)
Q Consensus        83 ~~kFid~Arq~E~fFL   98 (415)
                      ..+|+|-+-.+..|..
T Consensus       157 ~~~~~~~~~~~~~~~~  172 (1179)
T TIGR02168       157 RRAIFEEAAGISKYKE  172 (1179)
T ss_pred             HHHHHHHHccHHHHHH
Confidence            3444555544555543

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.

>smart00787 Spc7 Spc7 kinetochore protein

Probab=89.22  E-value=15  Score=37.20  Aligned_cols=39  Identities=15%  Similarity=0.211  Sum_probs=32.8

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy10214        213 IVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       213 vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~  251 (415)
                      ..+.++.++..+++.++.-|+...+++.++...++++++
T Consensus       222 ~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I~~ae~  260 (312)
T smart00787      222 IKVKKLEELEEELQELESKIEDLTNKKSELNTEIAEAEK  260 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            447788888888888888888888888888888888876

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

>PRK04863 mukB cell division protein MukB; Provisional

Probab=89.08  E-value=26  Score=42.49  Aligned_cols=32  Identities=16%  Similarity=0.256  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHh
Q psy10214        122 DIVDLRHDLARKEELIKRHYDKIAVWQNLLSD  153 (415)
Q Consensus       122 di~eLR~ElaRKnaLLrkhy~KIavWqnLlsd  153 (415)
                      +|.+.-.||.++-+.|++.+.+...|.++...
T Consensus       311 rI~diL~ELe~rL~kLEkQaEkA~kyleL~ee  342 (1486)
T PRK04863        311 EMARELAELNEAESDLEQDYQAASDHLNLVQT  342 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45555577777777778888877777777664

>KOG0995|consensus

Probab=88.79  E-value=43  Score=37.14  Aligned_cols=118  Identities=25%  Similarity=0.178  Sum_probs=66.2

Q ss_pred             hhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHH-----
Q psy10214         73 DEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVW-----  147 (415)
Q Consensus        73 ~E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavW-----  147 (415)
                      .|.+..+.--++||.+.-.+|+.==-..==.|+.++.|...||     .|+..|+.+..+..+-|.+..-..+.+     
T Consensus       265 re~~~~L~~D~nK~~~y~~~~~~k~~~~~~~l~~l~~Eie~kE-----eE~e~lq~~~d~Lk~~Ie~Q~iS~~dve~mn~  339 (581)
T KOG0995|consen  265 REKKARLQDDVNKFQAYVSQMKSKKQHMEKKLEMLKSEIEEKE-----EEIEKLQKENDELKKQIELQGISGEDVERMNL  339 (581)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHH
Confidence            4556667777889999999888754333345677788877777     355555555555554444332222222     


Q ss_pred             -----HHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHH
Q psy10214        148 -----QNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFL  199 (415)
Q Consensus       148 -----qnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFL  199 (415)
                           +.-++.+++.+..|++..-.    ...+|....+..-..|+++.......-|
T Consensus       340 Er~~l~r~l~~i~~~~d~l~k~vw~----~~l~~~~~f~~le~~~~~~~~l~~~i~l  392 (581)
T KOG0995|consen  340 ERNKLKRELNKIQSELDRLSKEVWE----LKLEIEDFFKELEKKFIDLNSLIRRIKL  392 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                 23344455555555554321    1333444444444677777766665555

>KOG4368|consensus

Probab=88.67  E-value=21  Score=39.93  Aligned_cols=28  Identities=14%  Similarity=0.195  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHhHHhHH
Q psy10214        128 HDLARKEELIKRHYDKIAVWQNLLSDLQ  155 (415)
Q Consensus       128 ~ElaRKnaLLrkhy~KIavWqnLlsdfQ  155 (415)
                      +|.++-+++|.+....++.++++|.++-
T Consensus        87 ~~~~~~~k~l~~~~l~~~~~~~~l~~~~  114 (757)
T KOG4368|consen   87 AVEQQMQKLLEETQLDMNEFDNLLQPII  114 (757)
T ss_pred             HHHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence            3445556777777777777777776654

>PTZ00009 heat shock 70 kDa protein; Provisional

Probab=88.64  E-value=5.3  Score=43.46  Aligned_cols=63  Identities=8%  Similarity=0.094  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHHHHHhhhcc-CchhhhHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHhc
Q psy10214        189 DLARQMEAFFLQKRFLLSAL-KPELIVKEDIVDLRHDLARKEELIK--------RHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       189 D~ARQLE~FFLQKrlllSa~-KPe~vvKEEI~dLK~ELqRKErLIq--------Kh~eKIeeWQsvL~dlq~  251 (415)
                      +.-..+|.|.+..+-+++.. ..+.+..++..+|+..+++.++||.        .+.+|+++-+.+++.+..
T Consensus       539 eakN~lEs~Iy~~r~~L~~~~~~~~~t~ee~~~l~~~l~~~~~wL~~~~~~~~~~~~~kl~eL~~~~~pi~~  610 (653)
T PTZ00009        539 EAKNGLENYCYSMKNTLQDEKVKGKLSDSDKATIEKAIDEALEWLEKNQLAEKEEFEHKQKEVESVCNPIMT  610 (653)
T ss_pred             HHHhhhHHHHHHHHHHHhhhhhhccCCHHHHHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHH
Confidence            33356888888888777531 2334668888999999999999995        346777777777777754

>KOG3227|consensus

Probab=88.62  E-value=5.7  Score=39.08  Aligned_cols=12  Identities=42%  Similarity=0.420  Sum_probs=7.9

Q ss_pred             CCCCCCccccCC
Q psy10214        344 GGPSSGMMFMGP  355 (415)
Q Consensus       344 g~~~~~~~~~~~  355 (415)
                      .++++++|-+-.
T Consensus       164 ~gp~sq~m~~~~  175 (231)
T KOG3227|consen  164 AGPSSQQMPQQE  175 (231)
T ss_pred             CCcccccccccc
Confidence            556677777665

>PRK05771 V-type ATP synthase subunit I; Validated

Probab=88.56  E-value=7.2  Score=42.21  Aligned_cols=45  Identities=22%  Similarity=0.486  Sum_probs=27.1

Q ss_pred             HhhhhchhHHHHHHHHHHHHH---HHHHHhhhHHHHHHHhHHhHHHHh
Q psy10214        114 KEVNMVTKDIVDLRHDLARKE---ELIKRHYDKIAVWQNLLSDLQSCL  158 (415)
Q Consensus       114 ke~n~~~~di~eLR~ElaRKn---aLLrkhy~KIavWqnLlsdfQscL  158 (415)
                      ++++.+.+++.++.+++.+.+   +.+++..+.++.|.++.-++....
T Consensus        93 ~~~~~~~~~i~~l~~~~~~L~~~~~~l~~~~~~l~~~~~ld~~l~~~~  140 (646)
T PRK05771         93 EELEKIEKEIKELEEEISELENEIKELEQEIERLEPWGNFDLDLSLLL  140 (646)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCHHHhC
Confidence            344455555555555544444   445566667888988777775443

>KOG4302|consensus

Probab=88.45  E-value=21  Score=39.91  Aligned_cols=81  Identities=22%  Similarity=0.278  Sum_probs=49.8

Q ss_pred             hhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHH-------HHhhhhchhHHH-HHHHHHHHHHHHHHHhhhHH
Q psy10214         73 DEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELI-------VKEVNMVTKDIV-DLRHDLARKEELIKRHYDKI  144 (415)
Q Consensus        73 ~E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i-------~ke~n~~~~di~-eLR~ElaRKnaLLrkhy~KI  144 (415)
                      .+++.+..+-.+|.-|++.+|..++.  |+..|.-..+.+       +.++|..+-|+. .+++|+.|.++|=..+    
T Consensus       236 ~~l~~~k~qr~~kl~~l~~~~~~LWn--~l~ts~Ee~~~f~~~t~~e~t~~~~ls~d~I~~ve~Ev~Rl~qlK~s~----  309 (660)
T KOG4302|consen  236 KKLKEEKKQRLQKLQDLRTKLLELWN--LLDTSDEERQRFVHVTESEATEPNSLSLDIIEQVEKEVDRLEQLKASN----  309 (660)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH--hccCCHHHHHHHccccHHHhhccccccHHHHHHHHHHHHHHHHHHHHh----
Confidence            45667777777888888888887765  233333333333       567777666654 4778888887653333    


Q ss_pred             HHHHHhHHhHHHHhhhh
Q psy10214        145 AVWQNLLSDLQSCLQVL  161 (415)
Q Consensus       145 avWqnLlsdfQscLs~L  161 (415)
                        ..+|..+.+..|..|
T Consensus       310 --mKeli~k~r~Eleel  324 (660)
T KOG4302|consen  310 --MKELIEKKRSELEEL  324 (660)
T ss_pred             --HHHHHHHHHHHHHHH
Confidence              344555555555544

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

Probab=88.43  E-value=32  Score=40.29  Aligned_cols=23  Identities=13%  Similarity=0.263  Sum_probs=14.5

Q ss_pred             CCchhhHhHhHHHHHHHHHHHHH
Q psy10214         69 PLEKDEIKLEIDQATLKFLDLAR   91 (415)
Q Consensus        69 ~~~k~E~~~~veq~~~kFid~Ar   91 (415)
                      ..++++++..++.+.....++-.
T Consensus       599 ~~~ee~L~~~l~~~~~~l~~~~~  621 (1201)
T PF12128_consen  599 AASEEELRERLEQAEDQLQSAEE  621 (1201)
T ss_pred             hcChHHHHHHHHHHHHHHHHHHH
Confidence            45777888877766655444433

>TIGR00606 rad50 rad50

Probab=88.39  E-value=32  Score=40.52  Aligned_cols=16  Identities=6%  Similarity=0.171  Sum_probs=8.0

Q ss_pred             chhhHhHhHHHHHHHH
Q psy10214         71 EKDEIKLEIDQATLKF   86 (415)
Q Consensus        71 ~k~E~~~~veq~~~kF   86 (415)
                      +.+||..+++..=.++
T Consensus       823 s~~ele~ei~~~~~el  838 (1311)
T TIGR00606       823 TVQQVNQEKQEKQHEL  838 (1311)
T ss_pred             CHHHHHHHHHHHHHHH
Confidence            4456665555443333

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

>cd07639 BAR_ACAP1 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 1

Probab=88.30  E-value=16  Score=35.06  Aligned_cols=68  Identities=18%  Similarity=0.147  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHh
Q psy10214         79 IDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCL  158 (415)
Q Consensus        79 veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscL  158 (415)
                      +.-++.||.++-+.||+||-   .++..  -+.+|..      -+..+++|-=++=.-.||+|+|.  |+++..++...+
T Consensus        59 i~~~l~kFs~~l~ei~~~~~---~Ll~~--~~~~l~~------~L~~F~k~dl~~vKe~kK~FdK~--s~~~d~al~K~~  125 (200)
T cd07639          59 MAECLEKFSDGLNHILDSHA---ELLEA--TQFSFKQ------QLQLLVKEDLRGFRDARKEFERG--AESLEAALQHNA  125 (200)
T ss_pred             hHHHHHHHHHHHHHHHHHHH---HHHHH--HHHHHHH------HHHHHHHhhhHHHHHHhhhHhhc--chhHHHHHHHHh
Confidence            88899999999999999982   33322  3333333      45555444444445678889987  777777755444


Q ss_pred             h
Q psy10214        159 Q  159 (415)
Q Consensus       159 s  159 (415)
                      .
T Consensus       126 ~  126 (200)
T cd07639         126 E  126 (200)
T ss_pred             h
Confidence            3

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ACAP1 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 1), also called centaurin beta-1, is an Arf6-specific GTPase activating protein (GAP) which mediates Arf6 signaling. Arf6 is involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration. ACAP1 also participates in the cargo sorting and recycling of the transferrin receptor and integrin beta1. It may also play a role in innate immune responses. ACAP1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.

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

Probab=88.21  E-value=7.4  Score=39.72  Aligned_cols=53  Identities=30%  Similarity=0.365  Sum_probs=38.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-h------c-----------ccCCCCCCCCCCCC
Q psy10214        213 IVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDL-Q------G-----------WAKSPAHQGSTSSA  265 (415)
Q Consensus       213 vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dl-q------~-----------~~~spaq~~~~~~~  265 (415)
                      -+|+-|+-+|.-|..||.=|+||+-.|..-..-|+-| +      +           .+.||+..++.+++
T Consensus       128 QLkQvieTmrssL~ekDkGiQKYFvDINiQN~KLEsLLqsMElAq~g~~rde~~l~~~c~SP~~sLt~sst  198 (305)
T PF15290_consen  128 QLKQVIETMRSSLAEKDKGIQKYFVDINIQNKKLESLLQSMELAQSGSLRDEGCLDFSCDSPAKSLTRSST  198 (305)
T ss_pred             HHHHHHHHHHhhhchhhhhHHHHHhhhhhhHhHHHHHHHHHHHHHhccccccCCcCCccCCcccccccccc
Confidence            5688888888899999999999999988754444443 1      1           45677777766553

>cd07637 BAR_ACAP3 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 3

Probab=87.65  E-value=26  Score=33.41  Aligned_cols=108  Identities=16%  Similarity=0.167  Sum_probs=63.6

Q ss_pred             chhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHH
Q psy10214        119 VTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFF  198 (415)
Q Consensus       119 ~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FF  198 (415)
                      +..|+.+|+.+|.|..++++.-++-=..+.+....|=+.|..+...     +....    -|..++.+|.+..+.+++|.
T Consensus         7 ~E~~~~~le~~l~kl~K~~~~~~d~g~~~~~a~~~F~~~l~d~~~~-----~~gd~----~i~~~L~kF~~~l~ei~~~~   77 (200)
T cd07637           7 VETDVVEIEAKLDKLVKLCSGMIEAGKAYATTNKLFVSGIRDLSQQ-----CKKDE----MISECLDKFGDSLQEMVNYH   77 (200)
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCch----HHHHHHHHHHHHHHHHHHHH
Confidence            4568999999999988888877775434444444454555444332     22211    26677789999999998887


Q ss_pred             HHHHHhh--hccC-chhhhHHHHHHHHHHHHHHHHHHHHH
Q psy10214        199 LQKRFLL--SALK-PELIVKEDIVDLRHDLARKEELIKRH  235 (415)
Q Consensus       199 LQKrlll--Sa~K-Pe~vvKEEI~dLK~ELqRKErLIqKh  235 (415)
                      .-..-..  +... -...+++||..+|..=.+-|+.-++|
T Consensus        78 ~~l~~q~e~~l~~pL~~F~k~dL~~~KE~rK~Fdk~se~y  117 (200)
T cd07637          78 MILFDQAQRSVRQQLHSFVKEDVRKFKETKKQFDKVREDL  117 (200)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            6332111  1111 23356777777765443334433333

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ACAP3 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 3), also called centaurin beta-5, is presumed to be an Arf GTPase activating protein (GAP) based on its similarity to the Arf6-specific GAPs ACAP1 and ACAP2. The specific function of ACAP3 is still unknown. ACAP3 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.

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

Probab=87.47  E-value=67  Score=37.80  Aligned_cols=42  Identities=19%  Similarity=0.336  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHhcccCCC
Q psy10214        215 KEDIVDLRHDLA-RKEELIKRHYDKIAVWQNLLSDLQGWAKSP  256 (415)
Q Consensus       215 KEEI~dLK~ELq-RKErLIqKh~eKIeeWQsvL~dlq~~~~sp  256 (415)
                      .+++..+..++. +.+..+.++......++.-+..++..+++|
T Consensus       419 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~  461 (1201)
T PF12128_consen  419 EEEYQALEQELRQQSQEQLEELQEQREQLKSELAELKQQLKNP  461 (1201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            344445555544 455556666666666666666666555533

>PRK05560 DNA gyrase subunit A; Validated

Probab=87.38  E-value=12  Score=42.06  Aligned_cols=128  Identities=15%  Similarity=0.252  Sum_probs=71.2

Q ss_pred             cChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHH---HHhhhhhcccccccccchhhHhHhHHHH
Q psy10214        107 LKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQ---SCLQVLTKEDEVSTTLEKDEIKLEIDQA  183 (415)
Q Consensus       107 ~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQ---scLs~LSkqE~ser~~DqdEIKv~VEq~  183 (415)
                      ...+.|++||=.+|.++-..|.+..-+...     .++++...+.-++.   ..+..+.+.      -+.+|++..+.  
T Consensus       340 ~~~~~il~~~~~~r~~~~~~r~~~~l~~~~-----~~~~~l~g~~~~~~~~d~vI~iir~s------~~~~~~~~~L~--  406 (805)
T PRK05560        340 LNLKEILEAFLEHRKEVITRRTRFELRKAE-----ERAHILEGLLIALDNIDEVIALIRAS------PTPAEAKEGLM--  406 (805)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHhhHHHHHHHHcC------CCHHHHHHHHH--
Confidence            457889999999988888877665444433     34433333333322   222222111      13344443333  


Q ss_pred             HHHHHHHH-HHHHHHHHHHHH-hhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy10214        184 TLKFLDLA-RQMEAFFLQKRF-LLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       184 tnRFLD~A-RQLE~FFLQKrl-llSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~  251 (415)
                       .+| +.. .+.| +-|..++ .+|...-+ -+++|+.+|+.||++.+.+|....+.++.|..-|.++..
T Consensus       407 -~~f-~~~~~qa~-~IL~m~L~~LT~~e~~-kL~~E~~~l~~ei~~l~~iL~~~~~l~~~i~~EL~~ikk  472 (805)
T PRK05560        407 -ERF-GLSEIQAQ-AILDMRLQRLTGLERD-KIEDEYKELLALIADLKDILASPERLLEIIKEELLEIKE  472 (805)
T ss_pred             -Hhc-CCCHHHHH-HHHHhHHHHHhHHHHH-HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence             222 111 1221 2222222 12222222 347889999999999999998888888888888888855

>KOG0999|consensus

Probab=87.23  E-value=41  Score=37.65  Aligned_cols=39  Identities=23%  Similarity=0.255  Sum_probs=18.9

Q ss_pred             hhhHhHhHHHHHHHHHHHHH-HHHHHHHHHHHhhhccCchhh
Q psy10214        173 KDEIKLEIDQATLKFLDLAR-QMEAFFLQKRFLLSALKPELI  213 (415)
Q Consensus       173 qdEIKv~VEq~tnRFLD~AR-QLE~FFLQKrlllSa~KPe~v  213 (415)
                      .+|++..-.+-..-+-+|+- .=|+.-|||.+  |.++..+|
T Consensus       155 r~elKe~KfRE~RllseYSELEEENIsLQKqV--s~LR~sQV  194 (772)
T KOG0999|consen  155 RDELKEYKFREARLLSEYSELEEENISLQKQV--SNLRQSQV  194 (772)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcchHHHHH--HHHhhhhh
Confidence            44555444433333334442 33456777743  55555554

>cd07638 BAR_ACAP2 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 2

Probab=86.51  E-value=25  Score=33.78  Aligned_cols=108  Identities=16%  Similarity=0.201  Sum_probs=68.7

Q ss_pred             chhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHH
Q psy10214        119 VTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFF  198 (415)
Q Consensus       119 ~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FF  198 (415)
                      +..|+.+|+.++.|.....++-++=-..+-+-...|-..|..+.+     .+.+.+    -+..++.+|.+.-+.+++|.
T Consensus         7 ~E~d~~~Le~~l~Kl~K~~~~~~dag~~~~~a~~~F~~~l~d~~~-----~~~~De----~i~~~l~kF~~~l~ei~~~~   77 (200)
T cd07638           7 VEGDVAELELKLDKLVKLCIGMIDAGKAFCQANKQFMNGIRDLAQ-----YSSKDA----VIETSLTKFSDTLQEMINYH   77 (200)
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH-----hCCcch----hhHHHHHHHHHHHHHHHHHH
Confidence            456999999999999999999998655555666777777777744     122222    45667788989888888875


Q ss_pred             H----HHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        199 L----QKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHY  236 (415)
Q Consensus       199 L----QKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~  236 (415)
                      -    |....+. .+-+..++++|.+.|..=.+-|+.-+++.
T Consensus        78 ~~L~~q~~~~l~-~~L~~F~k~dl~~vke~kk~FdK~s~~~~  118 (200)
T cd07638          78 TILFDQAQRSIK-AQLQTFVKEDLRKFKDAKKQFDKVSEEKE  118 (200)
T ss_pred             HHHHHHHHHHHH-HHHHHHHHHHhHHHHHHHHHHHHHhHHHH
Confidence            4    2221110 11233557777766665444444444433

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ACAP2 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 2), also called centaurin beta-2, is an Arf6-specific GTPase activating protein (GAP) which mediates Arf6 signaling. Arf6 is involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration. ACAP2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.

>cd07603 BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins

Probab=86.33  E-value=22  Score=33.79  Aligned_cols=61  Identities=16%  Similarity=0.174  Sum_probs=36.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhh--ccCc-hhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        179 EIDQATLKFLDLARQMEAFFLQKRFLLS--ALKP-ELIVKEDIVDLRHDLARKEELIKRHYDKI  239 (415)
Q Consensus       179 ~VEq~tnRFLD~ARQLE~FFLQKrlllS--a~KP-e~vvKEEI~dLK~ELqRKErLIqKh~eKI  239 (415)
                      .|..++.+|.+..+.+++++....-...  -..| +..+|+||..+|..=.+-|..-.+|...+
T Consensus        58 ~i~~~l~kF~~~l~el~~~~~~L~~q~~~~i~~pL~~F~k~dL~~vKE~kk~Fdk~s~~yd~al  121 (200)
T cd07603          58 LVQNCLNKFIQALQEMNNFHTILLDQAQRTVSTQLQNFVKEDIKKVKESKKHFEKISDDLDNAL  121 (200)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence            4567888999999999998774332111  1223 44668888877744444444444443333

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. Vertebrates contain at least three members, ACAP1, ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific GAPs, involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration, by mediating Arf6 signaling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.

>PF05600 DUF773: Protein of unknown function (DUF773); InterPro: IPR008491 This family contains several eukaryotic sequences which are thought to be CDK5 activator-binding proteins, however, the function of this family is unknown

Probab=85.89  E-value=24  Score=38.02  Aligned_cols=141  Identities=14%  Similarity=0.165  Sum_probs=83.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHH-HHHHHhhh-HHHHHHHhHHhHHHHh
Q psy10214         81 QATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKE-ELIKRHYD-KIAVWQNLLSDLQSCL  158 (415)
Q Consensus        81 q~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKn-aLLrkhy~-KIavWqnLlsdfQscL  158 (415)
                      .+=++|||=--.+|+|+-||...++. ....++..             -+..+. ..|+.+-. +|.   +++++.+.++
T Consensus       351 ~~R~~fldeL~EL~aFL~qRl~El~~-~~~~~l~~-------------~~~~~ap~~lq~~t~~~i~---~ml~~V~~ii  413 (507)
T PF05600_consen  351 ETRNQFLDELLELEAFLKQRLYELSN-EESSSLSF-------------SQFQNAPSILQQQTAESIE---EMLSAVEEII  413 (507)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhcc-cccchHHH-------------HHhhhccHHHHhcCHHHHH---HHHHHHHHHH
Confidence            45578999999999999999888864 22222222             111111 22332222 343   4477777888


Q ss_pred             hhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        159 QVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDK  238 (415)
Q Consensus       159 s~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eK  238 (415)
                      ..|+...-. +.........-||+.+..|....+..+.+-..+.          .+.+-+.++..++....--|....++
T Consensus       414 ~~Lt~~~~~-~L~~Ik~SprYvdrl~~~L~qk~~~~~k~~~~~~----------~l~~kr~e~~~e~~~l~pkL~~l~~~  482 (507)
T PF05600_consen  414 SQLTNPRTQ-HLFMIKSSPRYVDRLVESLQQKLKQEEKLRRKRE----------DLEEKRQEAQEEQQELEPKLDALVER  482 (507)
T ss_pred             HHhcCHHHH-HHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            877654321 2222333344477777777776666666554332          22444666666666666667777777


Q ss_pred             HHHHHHHHHHH
Q psy10214        239 IAVWQNLLSDL  249 (415)
Q Consensus       239 IeeWQsvL~dl  249 (415)
                      -++.|+.++.-
T Consensus       483 Tr~Lq~~iE~~  493 (507)
T PF05600_consen  483 TRELQKQIEAD  493 (507)
T ss_pred             HHHHHHHHHHH
Confidence            77777776653

>PF11867 DUF3387: Domain of unknown function (DUF3387); InterPro: IPR021810 This domain is functionally uncharacterised

Probab=85.77  E-value=36  Score=34.17  Aligned_cols=26  Identities=19%  Similarity=0.335  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy10214        226 ARKEELIKRHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       226 qRKErLIqKh~eKIeeWQsvL~dlq~  251 (415)
                      ++.+++|++|..+...|..+++.|-.
T Consensus       201 ErLe~iI~~Y~~~~i~~~e~~~eLi~  226 (335)
T PF11867_consen  201 ERLEEIIEKYNNRSISSEEVIEELIK  226 (335)
T ss_pred             HHHHHHHHHHHcccchHHHHHHHHHH
Confidence            46788888888887778888777744

This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with PF04851 from PFAM, PF04313 from PFAM.

>KOG4274|consensus

Probab=85.61  E-value=8.3  Score=42.79  Aligned_cols=13  Identities=31%  Similarity=0.437  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHH
Q psy10214        189 DLARQMEAFFLQK  201 (415)
Q Consensus       189 D~ARQLE~FFLQK  201 (415)
                      +.||+||+|++-|
T Consensus        32 k~a~~mE~hVF~K   44 (742)
T KOG4274|consen   32 KSAKDMESHVFLK   44 (742)
T ss_pred             cchHHHHHHHHHh
Confidence            6678999987744

>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family

Probab=85.48  E-value=2.2  Score=35.13  Aligned_cols=92  Identities=16%  Similarity=0.181  Sum_probs=46.5

Q ss_pred             HHHHHhhcChhHHHHhhhhchhHHHHHHHH-----HHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhhhcc-cccccccch
Q psy10214        100 KRFLLSALKPELIVKEVNMVTKDIVDLRHD-----LARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKE-DEVSTTLEK  173 (415)
Q Consensus       100 kr~~ls~~kpe~i~ke~n~~~~di~eLR~E-----laRKnaLLrkhy~KIavWqnLlsdfQscLs~LSkq-E~ser~~Dq  173 (415)
                      +...|+...-+.+-+||+.+..++..+..+     -.+-.+|+++|+.-+..|-....++..+|..+-.. +.+     .
T Consensus        21 ~~~~l~~~~~~~~~~~~~~l~~~l~~~~~~g~~p~s~evq~l~~~~~~~~~~~~~~~~~~~~~l~~~y~~~~~~-----~   95 (118)
T PF07739_consen   21 RLASLSKEEWQELQKEWDELFAELAALMEEGVDPDSPEVQELAERWMELINQFTGGDPELLRGLAQMYVEDPRF-----A   95 (118)
T ss_dssp             ------------TTHHHHHHHHHHHHHHHHT--TT-HHHHHHHHHHHHHHHHSS---HHHHHHHHHHTTSTHHH-----H
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCHHH-----H
Confidence            335555555666667777766666655554     12234888899988888877777777777766322 222     2


Q ss_pred             hhHhHhHHHHHHHHHHHHHHHHHHH
Q psy10214        174 DEIKLEIDQATLKFLDLARQMEAFF  198 (415)
Q Consensus       174 dEIKv~VEq~tnRFLD~ARQLE~FF  198 (415)
                      ..+...+...+.+||.  ++++.|+
T Consensus        96 ~~~~~~~~~~~~~fi~--~Ai~~y~  118 (118)
T PF07739_consen   96 AMYDKKFGPGLAEFIE--KAIEAYA  118 (118)
T ss_dssp             HHHG-GGSTTHHHHHH--HHHHHHH
T ss_pred             hhccccCCHHHHHHHH--HHHHHHC
Confidence            2223345556677777  6666664

The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.

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

Probab=85.20  E-value=3.4  Score=33.92  Aligned_cols=50  Identities=24%  Similarity=0.427  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHH-HhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhh
Q psy10214         92 QMEAFFLQKRFL-LSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHY  141 (415)
Q Consensus        92 q~E~fFLqkr~~-ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy  141 (415)
                      -+.-|||..|+. .+-.-.+.+++|--...-++..|++|+.++..+|++--
T Consensus        20 KLrI~fLee~l~~~~~~~~~~~~keNieLKve~~~L~~el~~~~~~l~~a~   70 (75)
T PF07989_consen   20 KLRIYFLEERLQKLGPESIEELLKENIELKVEVESLKRELQEKKKLLKEAE   70 (75)
T ss_pred             HHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            366799999998 44556678888844556678888899998888887644

>KOG4592|consensus

Probab=84.90  E-value=3  Score=46.27  Aligned_cols=31  Identities=29%  Similarity=0.669  Sum_probs=17.2

Q ss_pred             CCCCCCCCCCCCCCCcchhhHHhhccCCCCCC
Q psy10214        381 GNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPD  412 (415)
Q Consensus       381 ~~~~~~~~~~~~~~~~~la~le~~tsnig~~~  412 (415)
                      ++-+|-||+ |..+++|.-||-+.----|||.
T Consensus       219 ~s~~p~g~~-~~~vP~pvi~~pqmPlQ~gm~~  249 (728)
T KOG4592|consen  219 SSQQPNGIG-GNRVPPPVIYLPQMPLQQGMPH  249 (728)
T ss_pred             CccCccCCC-CCCCCCCccccccChhhcCCCC
Confidence            445555553 5667777777655443344443

>PF12252 SidE: Dot/Icm substrate protein; InterPro: IPR021014 This entry represents bacterial proteins that are typically between 397 and 1543 amino acids in length including SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria

Probab=84.83  E-value=13  Score=43.88  Aligned_cols=191  Identities=18%  Similarity=0.182  Sum_probs=109.6

Q ss_pred             ccchhHhhhhhhccccCCCCCCCCCCCCchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhH
Q psy10214         43 GLLQGPLAYLEKTTSNIGLPDGRSLSPLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKD  122 (415)
Q Consensus        43 ~~f~~~l~~~~~~~~~~~~~~~~~~~~~~k~E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~d  122 (415)
                      .|.+..|...||. .+.+..        ++-.=-++|..-|.+|-|.---+|- .-++|+..-.--.|-++.=      |
T Consensus      1175 kL~dAyl~eitKq-IsaLe~--------e~PKnltdvK~missf~d~laeiE~-LrnErIKkHGaSkePLDlS------D 1238 (1439)
T PF12252_consen 1175 KLYDAYLVEITKQ-ISALEK--------EKPKNLTDVKSMISSFNDRLAEIEF-LRNERIKKHGASKEPLDLS------D 1238 (1439)
T ss_pred             hhHHHHHHHHHHH-HHHHHh--------hCCCchhhHHHHHHHHHhhhhHHHH-HHHHHhhccCCCCCccchh------h
Confidence            4667777777775 333321        1111224777888899888888875 7888988877666666666      9


Q ss_pred             HHHHHHHHHHHH-----HHHHHhhhHHH-----HHHHhHHhHHHHhhhhhcccccccccc-hhhHhHhHHHHHHHHHHHH
Q psy10214        123 IVDLRHDLARKE-----ELIKRHYDKIA-----VWQNLLSDLQSCLQVLTKEDEVSTTLE-KDEIKLEIDQATLKFLDLA  191 (415)
Q Consensus       123 i~eLR~ElaRKn-----aLLrkhy~KIa-----vWqnLlsdfQscLs~LSkqE~ser~~D-qdEIKv~VEq~tnRFLD~A  191 (415)
                      |.+||.+|++-|     .||+.....++     -++.=+...|.||..|.+-+..-..++ ....+.++.+..+-|++.-
T Consensus      1239 lDkLk~~LQ~iNQ~LV~~LIn~iR~slnqme~~tf~~q~~eiq~n~~ll~~L~~tlD~S~~a~Kqk~di~kl~~~lv~kQ 1318 (1439)
T PF12252_consen 1239 LDKLKGQLQKINQNLVKALINTIRVSLNQMEVKTFEEQEKEIQQNLQLLDKLEKTLDDSDTAQKQKEDIVKLNDFLVEKQ 1318 (1439)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999998     45555544333     333445566777776644332101111 1223444555555555543


Q ss_pred             H----------HHHHHHHHHHHhhhc----------cCchhhhHH----------------------HHHHHHHHHHHHH
Q psy10214        192 R----------QMEAFFLQKRFLLSA----------LKPELIVKE----------------------DIVDLRHDLARKE  229 (415)
Q Consensus       192 R----------QLE~FFLQKrlllSa----------~KPe~vvKE----------------------EI~dLK~ELqRKE  229 (415)
                      +          .+|++..|.|.+-.+          .|-+.+-+.                      ...+=+.+|+.|+
T Consensus      1319 KAYP~M~QlQ~ksealI~qLRelC~~h~~~l~k~~~~r~~el~~~~~e~Gi~~~~~~~~~~~t~~iglt~der~~i~~K~ 1398 (1439)
T PF12252_consen 1319 KAYPAMVQLQFKSEALIIQLRELCEAHQDNLAKTRKTRLQELTKQDREGGITGMVGNMFQGLTDYIGLTTDERLEIAMKQ 1398 (1439)
T ss_pred             hhchHHHHHhhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhccccccchhhhhhHHHHhhhhhhccchhHHHHHHHHH
Confidence            3          346666666654322          111111111                      1122356677777


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q psy10214        230 ELIKRHYDKIAVWQNLLSDL  249 (415)
Q Consensus       230 rLIqKh~eKIeeWQsvL~dl  249 (415)
                      +.+++.++.+..=+.-+++|
T Consensus      1399 ~~l~~fk~~Lnndk~di~qL 1418 (1439)
T PF12252_consen 1399 QSLARFKTDLNNDKYDIDQL 1418 (1439)
T ss_pred             HHHHHHHHhhccCcccHHHH
Confidence            77777777776655555555

There is little literature describing the family.

>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly

Probab=84.65  E-value=7.9  Score=32.52  Aligned_cols=35  Identities=23%  Similarity=0.370  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        215 KEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDL  249 (415)
Q Consensus       215 KEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dl  249 (415)
                      +..+..|..+++..+.-+.+..++++.++..++.+
T Consensus        93 ~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~~  127 (129)
T cd00890          93 KKRLETLEKQIEKLEKQLEKLQDQITELQEELQQL  127 (129)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44556666666666666666667777776666654

The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.

>cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II

Probab=84.40  E-value=37  Score=36.14  Aligned_cols=47  Identities=13%  Similarity=0.171  Sum_probs=29.4

Q ss_pred             cChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHh
Q psy10214        107 LKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCL  158 (415)
Q Consensus       107 ~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscL  158 (415)
                      +..+.|+++|=.+|.++-..|.+.     +|++...++++..++.-++..+.
T Consensus       315 ~~l~~iL~~f~~~R~~~~~rR~~~-----~l~k~~~rl~il~g~~~~i~~id  361 (445)
T cd00187         315 LNLKEILQEFLDHRLEVYTRRKEY-----ELGKAEARLHILEGLLKAILNID  361 (445)
T ss_pred             eCHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHhHHHHHHHHH
Confidence            457889999888888777665544     44455555555555555554443

DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.

>PF05427 FIBP: Acidic fibroblast growth factor binding (FIBP) ; InterPro: IPR008614 Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that is thought to be involved in the intracellular function of aFGF []

Probab=84.16  E-value=18  Score=37.92  Aligned_cols=80  Identities=23%  Similarity=0.331  Sum_probs=55.9

Q ss_pred             chhHHHHHHHHHHHHHHHHHHhhh--------HHH--HHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHH
Q psy10214        119 VTKDIVDLRHDLARKEELIKRHYD--------KIA--VWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFL  188 (415)
Q Consensus       119 ~~~di~eLR~ElaRKnaLLrkhy~--------KIa--vWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFL  188 (415)
                      |-.|+-|+|.=+.+|+. |.+|..        ++.  ..+++++.|.+..+.|..-..  +.++..|++.--+-.+.|||
T Consensus       229 FlqdLRdlK~ll~~k~~-ld~hk~lV~~~L~~~l~~~~l~elesnFK~l~Ralv~Ia~--gLs~sKElRdlF~DLvEK~I  305 (361)
T PF05427_consen  229 FLQDLRDLKTLLNDKDE-LDQHKHLVCRRLKGKLSERSLQELESNFKSLSRALVNIAS--GLSHSKELRDLFEDLVEKFI  305 (361)
T ss_pred             HHHHHHHHHHHhcChhH-HHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHh--cCCccHHHHHHHHHHHHHHh
Confidence            45588888876655443 344433        444  677889999988888755432  56788999888777889999


Q ss_pred             HHHH-------HHHHHHHHH
Q psy10214        189 DLAR-------QMEAFFLQK  201 (415)
Q Consensus       189 D~AR-------QLE~FFLQK  201 (415)
                      +..|       +++.||-..
T Consensus       306 EPlr~~~Wt~~dl~~FL~ay  325 (361)
T PF05427_consen  306 EPLRQAGWTKEDLRLFLSAY  325 (361)
T ss_pred             HHHHHCCCCHHHHHHHHHHH
Confidence            9996       566666533

; GO: 0017134 fibroblast growth factor binding

>KOG1854|consensus

Probab=84.11  E-value=79  Score=35.61  Aligned_cols=113  Identities=18%  Similarity=0.238  Sum_probs=57.5

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHH
Q psy10214         77 LEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQS  156 (415)
Q Consensus        77 ~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQs  156 (415)
                      +-||+--..|+|. +..|.||+.+-+.=-.+.-+-+.++         ++-.|+.+-+..|+.+..|+...  ..++..+
T Consensus       325 ~rvdql~~~l~d~-k~~~~~~~~~aiEk~Rl~~~~a~~~---------~~~~~~~~h~~~~~~E~~~~~~~--~~~~~~~  392 (657)
T KOG1854|consen  325 TRVDQLQKELEDQ-KADEELHIKRAIEKQRLQDSRALRA---------QLEYELEAHRRELQQELFKLIEE--IRSSSKN  392 (657)
T ss_pred             HHHHHHHHHHHHh-hhhhHHHHHHHHHHHhhhhHhhhHH---------HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHH
Confidence            3344443444431 2235578776554434443333333         34444444444455555443222  2333333


Q ss_pred             Hhh-hhhcccccccccchhhHhHhHHHHHHHH-HHHHHHHHHHHHHHHHhh
Q psy10214        157 CLQ-VLTKEDEVSTTLEKDEIKLEIDQATLKF-LDLARQMEAFFLQKRFLL  205 (415)
Q Consensus       157 cLs-~LSkqE~ser~~DqdEIKv~VEq~tnRF-LD~ARQLE~FFLQKrlll  205 (415)
                      .++ .|..+...    +-|.|+.-|.+.-+.| |+-.+.+|.-.||.|-+.
T Consensus       393 el~~ql~~qa~a----h~dhik~vvr~q~q~~~~e~~~~~~e~~l~ernl~  439 (657)
T KOG1854|consen  393 ELRNQLKRQAKA----HLDHIKDVVRQQEQLLTIEFKQKLEEAVLQERNLH  439 (657)
T ss_pred             HHHHHHHHHHHH----HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcch
Confidence            333 23222322    5677777777655555 566688999899887655

>KOG2129|consensus

Probab=83.95  E-value=69  Score=34.82  Aligned_cols=36  Identities=17%  Similarity=0.247  Sum_probs=23.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        214 VKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDL  249 (415)
Q Consensus       214 vKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dl  249 (415)
                      +.+|-.+.+.|.+|..+.|.+-.+|.+.--.+|++-
T Consensus       283 y~~Ee~~~reen~rlQrkL~~e~erRealcr~lsEs  318 (552)
T KOG2129|consen  283 YRAEEVDHREENERLQRKLINELERREALCRMLSES  318 (552)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            355666677777777777777777776655555544

>PF13514 AAA_27: AAA domain

Probab=83.81  E-value=93  Score=36.16  Aligned_cols=165  Identities=18%  Similarity=0.252  Sum_probs=77.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhcCh-------hHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhH
Q psy10214         82 ATLKFLDLARQMEAFFLQKRFLLSALKP-------ELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDL  154 (415)
Q Consensus        82 ~~~kFid~Arq~E~fFLqkr~~ls~~kp-------e~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdf  154 (415)
                      .-.+.-.+-+.++.|.-+-..++..+.+       +..+.++...-++..+...++.+.++-|.+.-..+..+..-++.+
T Consensus       748 ~~~ri~~~~~~~~~f~~~~~~L~~~l~~~~~~~~~~~~~~~L~~~l~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~  827 (1111)
T PF13514_consen  748 LRRRIEQMEADLAAFEEQVAALAERLGPDLPEDPAEEALEALRARLEEAREAQEERERLQEQLEELEEELEQAEEELEEL  827 (1111)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcCcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444555666677666666666555       234443333222333333444444555555555666666666666


Q ss_pred             HHHhhhhhcccccccccchhhHhHhHHH------HHHHHHHHHHHHHH----HHH-HHHHhhhccCchhhhHHHHHHHHH
Q psy10214        155 QSCLQVLTKEDEVSTTLEKDEIKLEIDQ------ATLKFLDLARQMEA----FFL-QKRFLLSALKPELIVKEDIVDLRH  223 (415)
Q Consensus       155 QscLs~LSkqE~ser~~DqdEIKv~VEq------~tnRFLD~ARQLE~----FFL-QKrlllSa~KPe~vvKEEI~dLK~  223 (415)
                      +..+..|....   ++.+.+++...+++      ...+.-+.-++++.    ..+ .....+...-+. .++.++.+++.
T Consensus       828 ~~~l~~L~~~a---~~~~~e~l~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~l~~e~~~~d~~-~l~~~l~~l~~  903 (1111)
T PF13514_consen  828 EAELAELLEQA---GVEDEEELREAEERAEERRELREELEDLERQLERQADGLDLEELEEELEELDPD-ELEAELEELEE  903 (1111)
T ss_pred             HHHHHHHHHhc---cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhhccCHH-HHHHHHHHHHH
Confidence            66665553322   23334444332221      11111111122211    000 000011111111 23566777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy10214        224 DLARKEELIKRHYDKIAVWQNLLSDLQ  250 (415)
Q Consensus       224 ELqRKErLIqKh~eKIeeWQsvL~dlq  250 (415)
                      ++++.+.-+....+++...+.-|+.+.
T Consensus       904 ~l~~l~~~~~~l~~~~~~~~~~l~~l~  930 (1111)
T PF13514_consen  904 ELEELEEELEELQEERAELEQELEALE  930 (1111)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            777777777777777777666666664

>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=83.67  E-value=83  Score=35.50  Aligned_cols=86  Identities=22%  Similarity=0.221  Sum_probs=45.4

Q ss_pred             chhhHhHhHHHHHHHHHH----HHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHH
Q psy10214         71 EKDEIKLEIDQATLKFLD----LARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAV  146 (415)
Q Consensus        71 ~k~E~~~~veq~~~kFid----~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIav  146 (415)
                      +.+|..--+-++++.|-+    .... =.+-+++|..+-..+-|+-++|.+    ++.+.++++..+.+.|.+-|+.|..
T Consensus       533 ~~~E~l~lL~~a~~vlreeYi~~~~~-ar~ei~~rv~~Lk~~~e~Ql~~L~----~l~e~~~~l~~~ae~LaeR~e~a~d  607 (717)
T PF10168_consen  533 SPQECLELLSQATKVLREEYIEKQDL-AREEIQRRVKLLKQQKEQQLKELQ----ELQEERKSLRESAEKLAERYEEAKD  607 (717)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555556677777633    2211 135577887765555555556533    4444555555566666666665554


Q ss_pred             HHHhHH-hHHHHhhhh
Q psy10214        147 WQNLLS-DLQSCLQVL  161 (415)
Q Consensus       147 WqnLls-dfQscLs~L  161 (415)
                      -++.+. -++.++..+
T Consensus       608 ~Qe~L~~R~~~vl~~l  623 (717)
T PF10168_consen  608 KQEKLMKRVDRVLQLL  623 (717)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            443322 244444433

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 [].

>KOG0964|consensus

Probab=83.66  E-value=51  Score=38.99  Aligned_cols=67  Identities=27%  Similarity=0.245  Sum_probs=35.2

Q ss_pred             hcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        162 TKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAV  241 (415)
Q Consensus       162 SkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIee  241 (415)
                      .++..-..-+.++|-+.||.   +.++++.+.+...          ...+.+++.||.+++.++..+.+-|+++-.-|.+
T Consensus       377 ~Kqgr~sqFssk~eRDkwir---~ei~~l~~~i~~~----------ke~e~~lq~e~~~~e~~l~~~~e~i~~l~~si~e  443 (1200)
T KOG0964|consen  377 AKQGRYSQFSSKEERDKWIR---SEIEKLKRGINDT----------KEQENILQKEIEDLESELKEKLEEIKELESSINE  443 (1200)
T ss_pred             HhhccccccCcHHHHHHHHH---HHHHHHHHHHhhh----------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhh
Confidence            44433335677889999988   3334433322221          1123344556666666665555555555554443

>PF07426 Dynactin_p22: Dynactin subunit p22; InterPro: IPR009991 This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport

Probab=83.59  E-value=39  Score=31.67  Aligned_cols=90  Identities=14%  Similarity=0.260  Sum_probs=53.0

Q ss_pred             HHHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhhccCchhhhHHHHHHHH
Q psy10214        143 KIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLR  222 (415)
Q Consensus       143 KIavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK  222 (415)
                      |+++.-.-+++++...+.|.+-..++...|.+.+     ++|..+.+.-..|....++...         ...+-..++.
T Consensus        85 K~~~ILa~e~~i~~~~~~Leki~~L~pvL~se~i-----~~vp~~~~kL~~L~~~~~~Q~e---------~~~~ls~~~~  150 (174)
T PF07426_consen   85 KLQIILAEEDEIKSTAELLEKIKSLEPVLDSESI-----RNVPELCDKLQKLSQIHLEQQE---------ESEELSEEVQ  150 (174)
T ss_pred             HHHHHHHccHHHHHHHHHHHHHHHhhhhcCcHHH-----hhhHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHH
Confidence            5555556666666666655554445455665555     2333333444445544443222         2244456666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        223 HDLARKEELIKRHYDKIAVWQNLL  246 (415)
Q Consensus       223 ~ELqRKErLIqKh~eKIeeWQsvL  246 (415)
                      .=++++..++....++..+|..+|
T Consensus       151 ~Ll~~YN~ii~~lSk~Fv~wD~~l  174 (174)
T PF07426_consen  151 ELLQQYNKIILLLSKQFVQWDEIL  174 (174)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcC
Confidence            668888888888888888898764

Dynactin localises to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis [].

>KOG0250|consensus

Probab=83.54  E-value=71  Score=37.85  Aligned_cols=51  Identities=16%  Similarity=0.251  Sum_probs=30.8

Q ss_pred             HHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhhh
Q psy10214        112 IVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLT  162 (415)
Q Consensus       112 i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~LS  162 (415)
                      +.+++|+..+.|...+..+.+..+.|++.|.|++-...-+..++.-+..+.
T Consensus       279 ~~~ql~~~~~~i~~~qek~~~l~~ki~~~~~k~~~~r~k~teiea~i~~~~  329 (1074)
T KOG0250|consen  279 VERQLNNQEEEIKKKQEKVDTLQEKIEEKQGKIEEARQKLTEIEAKIGELK  329 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            344555555555555555556667777777777777655566665555543

>PRK10350 hypothetical protein; Provisional

Probab=83.52  E-value=0.29  Score=44.71  Aligned_cols=46  Identities=26%  Similarity=0.231  Sum_probs=24.6

Q ss_pred             CCCcHHHHHHHHHHHHHHHhhhh------cCCCCCCCC--CCCCCCCCCccccC
Q psy10214        309 SGMPQQQQQVQMQQQIHMQHMQQ------QGMGPGGPP--SGPGGPSSGMMFMG  354 (415)
Q Consensus       309 ~~~~qq~qq~q~q~~~~~q~~~q------~~~~~~~~p--~~~g~~~~~~~~~~  354 (415)
                      ..+.|++|+|.+.+|+++|.++.      ++.++|+.+  .++=.-..+||.-+
T Consensus        52 ~~LnQqlq~Qtq~qQQ~LQ~Ql~~n~QRiqq~qPgn~~~~~Q~LpN~nGGML~~  105 (145)
T PRK10350         52 GMLNQQLKTQTRLQQQHLQNQINNNSQRVQQGQPGNNPARQQMLPNTNGGMLNS  105 (145)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccccCcCCCCccccC
Confidence            33444445555556666666553      456666643  44444556677633

>PF04108 APG17: Autophagy protein Apg17 ; InterPro: IPR007240 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=83.51  E-value=60  Score=33.78  Aligned_cols=53  Identities=15%  Similarity=0.113  Sum_probs=32.3

Q ss_pred             chhHhhhhhhccccCCCCC--CCCCCCCchhhHhHhHHHHHHHHHHHHHHHHHHHHH
Q psy10214         45 LQGPLAYLEKTTSNIGLPD--GRSLSPLEKDEIKLEIDQATLKFLDLARQMEAFFLQ   99 (415)
Q Consensus        45 f~~~l~~~~~~~~~~~~~~--~~~~~~~~k~E~~~~veq~~~kFid~Arq~E~fFLq   99 (415)
                      ||.|...+.-+|+......  .+.+.|+.+|-  .+|+-++...-+....||+.+..
T Consensus       219 fDqC~~a~~~~eg~~~~~~e~~e~l~Vl~~Da--~El~~V~~el~~~~~~~~~~~~~  273 (412)
T PF04108_consen  219 FDQCVTAVRHTEGEPMSEEERQEMLEVLENDA--QELPDVVKELQERLDEMENNEER  273 (412)
T ss_pred             HHHHHHHHHHhccCCCChHHHHHHHHHHHcch--hhHHHHHHHHHHHHHHHHHHHHH
Confidence            6777777766655222211  22333444442  35677788888888888888877

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 []. Autophagy protein 17 (Apg17) is required for activating Apg1 protein kinases. This entry also contains Autophagy protein 11 which is involved in cytoplasm to vacuole transport (Cvt) and pexophagy. ; GO: 0006914 autophagy

>PF11657 Activator-TraM: Transcriptional activator TraM

Probab=83.48  E-value=30  Score=31.92  Aligned_cols=71  Identities=18%  Similarity=0.207  Sum_probs=44.7

Q ss_pred             hHHHHHHHHHHHHH-----------------HHHHHhhhHHHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHH
Q psy10214        121 KDIVDLRHDLARKE-----------------ELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQA  183 (415)
Q Consensus       121 ~di~eLR~ElaRKn-----------------aLLrkhy~KIavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~  183 (415)
                      +.+.++.+|+++|.                 +.+=+.|.+.  -++.++.|...|..++.+       -.++.|...|+.
T Consensus         3 dk~~eiI~~IA~khgI~L~~DDPILil~TiNe~ll~~~~~a--q~~~l~~fk~elE~~~~~-------w~~dak~kAEki   73 (144)
T PF11657_consen    3 DKIEEIIAEIARKHGIALSRDDPILILQTINERLLEDSAKA--QQEQLDQFKEELEEIASR-------WGEDAKEKAEKI   73 (144)
T ss_pred             cHHHHHHHHHHHHcCCccCCCCchHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHH
Confidence            46778888888885                 2222223222  256677777777666443       345778888999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q psy10214        184 TLKFLDLARQMEAFFLQ  200 (415)
Q Consensus       184 tnRFLD~ARQLE~FFLQ  200 (415)
                      ++..+.+++.-=.-+++
T Consensus        74 L~aal~~ske~m~~~l~   90 (144)
T PF11657_consen   74 LNAALAASKEAMNKILQ   90 (144)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99998888654333343

>PF06248 Zw10: Centromere/kinetochore Zw10; InterPro: IPR009361 Zeste white 10 (ZW10) was initially identified as a mitotic checkpoint protein involved in chromosome segregation, and then implicated in targeting cytoplasmic dynein and dynactin to mitotic kinetochores, but it is also important in non-dividing cells

Probab=83.40  E-value=50  Score=35.48  Aligned_cols=34  Identities=15%  Similarity=0.173  Sum_probs=24.2

Q ss_pred             chhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214         71 EKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLL  104 (415)
Q Consensus        71 ~k~E~~~~veq~~~kFid~Arq~E~fFLqkr~~l  104 (415)
                      -|+||+..|+..-..|+......+..-.+-+.+.
T Consensus        26 ~k~eV~~~I~~~y~df~~~~~~~~~L~~~~~~l~   59 (593)
T PF06248_consen   26 LKEEVHSMINKKYSDFSPSLQSAKDLIERSKSLA   59 (593)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            3677777777777888888888877765554443

These include cytoplasmic dynein targeting to Golgi and other membranes, and SNARE-mediated ER-Golgi trafficking [, ]. Dominant-negative ZW10, anti-ZW10 antibody, and ZW10 RNA interference (RNAi) cause Golgi dispersal. ZW10 RNAi also disperse endosomes and lysosomes []. Drosophila kinetochore components Rough deal (Rod) and Zw10 are required for the proper functioning of the metaphase checkpoint in flies []. The eukaryotic spindle assembly checkpoint (SAC) monitors microtubule attachment to kinetochores and prevents anaphase onset until all kinetochores are aligned on the metaphase plate. It is an essential surveillance mechanism that ensures high fidelity chromosome segregation during mitosis. In higher eukaryotes, cytoplasmic dynein is involved in silencing the SAC by removing the checkpoint proteins Mad2 and the Rod-Zw10-Zwilch complex (RZZ) from aligned kinetochores [, , ].; GO: 0007067 mitosis, 0000775 chromosome, centromeric region, 0005634 nucleus

>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=83.33  E-value=91  Score=35.70  Aligned_cols=28  Identities=25%  Similarity=0.443  Sum_probs=17.0

Q ss_pred             hhhhchhHHHHHHHHHHHHHHHHHHhhh
Q psy10214        115 EVNMVTKDIVDLRHDLARKEELIKRHYD  142 (415)
Q Consensus       115 e~n~~~~di~eLR~ElaRKnaLLrkhy~  142 (415)
                      +++++..|+..||.++.+|+..|.+--.
T Consensus       337 ~~~~Lqsdve~Lr~rle~k~~~l~kk~~  364 (775)
T PF10174_consen  337 EAEMLQSDVEALRFRLEEKNSQLEKKQA  364 (775)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            3556666666666666666665555443

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 [].

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

Probab=83.29  E-value=26  Score=29.46  Aligned_cols=32  Identities=3%  Similarity=0.063  Sum_probs=22.3

Q ss_pred             HHHHhhhhchhHHHHHHHHHHHHHHHHHHhhh
Q psy10214        111 LIVKEVNMVTKDIVDLRHDLARKEELIKRHYD  142 (415)
Q Consensus       111 ~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~  142 (415)
                      .++.+||..++++..+-.++++.+.-+++|..
T Consensus         3 ~~~~~~q~l~~~~~~l~~~~~~l~~~~~E~~~   34 (105)
T cd00632           3 EQLAQLQQLQQQLQAYIVQRQKVEAQLNENKK   34 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46667777777777777777777766666644

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

>TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit, Gram-positive

Probab=83.28  E-value=15  Score=41.19  Aligned_cols=130  Identities=12%  Similarity=0.168  Sum_probs=71.5

Q ss_pred             ChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHH
Q psy10214        108 KPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKF  187 (415)
Q Consensus       108 kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRF  187 (415)
                      ..+.|+++|=.+|.++-..|.+.     +|++-..|+++...++.++.. +..+.+--.  ...+.+|++..+.   .+|
T Consensus       338 ~l~~il~~~~~~R~~~~~rr~~~-----~l~k~~~r~~il~g~~~~~~~-id~~i~iir--~~~~~~~~~~~l~---~~f  406 (738)
T TIGR01061       338 GLLSYLDAYIKHCHEVIINRSKY-----ELEKASKRLEIVEGLIKAISI-IDEIIKLIR--SSEDKSDAKENLI---DNF  406 (738)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHh-hhhHhHHHH--cCCCHHHHHHHHH---Hhc
Confidence            45788999888888877665544     444555556666555555552 222111000  0113334443332   222


Q ss_pred             HHHH-HHHHHHHHHHHH-hhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy10214        188 LDLA-RQMEAFFLQKRF-LLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       188 LD~A-RQLE~FFLQKrl-llSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~  251 (415)
                       ... .+.| +-|..++ .++.+.-+ -+++|+.+|+.||++.+.+|....+..+.|..-|.++..
T Consensus       407 -~~~~~q~~-~il~m~l~~lt~~e~~-kl~~e~~~l~~~i~~l~~iL~~~~~~~~~i~~el~~ik~  469 (738)
T TIGR01061       407 -KFTENQAE-AIVSLRLYRLTNTDIF-ELKEEQNELEKKIISLEQIIASEKARNKLLKKQLEEYKK  469 (738)
T ss_pred             -CCCHHHHH-HHHhhHHHHHhHHHHH-HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence             000 1211 2232222 12222222 337788888889999999888888888888888888854

Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason.

>PF09731 Mitofilin: Mitochondrial inner membrane protein; InterPro: IPR019133 Mitofilin controls mitochondrial cristae morphology

Probab=83.28  E-value=59  Score=34.63  Aligned_cols=18  Identities=28%  Similarity=0.724  Sum_probs=7.3

Q ss_pred             HHHHHHHHHHHHHHHhhh
Q psy10214        125 DLRHDLARKEELIKRHYD  142 (415)
Q Consensus       125 eLR~ElaRKnaLLrkhy~  142 (415)
                      +++.|..++.+.|++.|.
T Consensus       311 ~~~~e~~~~~~~l~~~~~  328 (582)
T PF09731_consen  311 ELREEFEREREELEEKYE  328 (582)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            444444444444444333

Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex []. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence (residues 1-43) rich in positive-charged and hydroxylated residues and a membrane anchor domain (residues 47-66). In addition, it has three centrally located coiled coil domains (residues 200-240,280-310 and 400-420) []. ; GO: 0031305 integral to mitochondrial inner membrane

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

Probab=83.21  E-value=49  Score=32.56  Aligned_cols=34  Identities=26%  Similarity=0.170  Sum_probs=15.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHH
Q psy10214        122 DIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQ  155 (415)
Q Consensus       122 di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQ  155 (415)
                      ....+++++...++.|......++.+++-++..+
T Consensus       138 ~~~~~~~~~~~l~~~i~~~~~~i~~~~~~l~~~~  171 (423)
T TIGR01843       138 RKSTLRAQLELILAQIKQLEAELAGLQAQLQALR  171 (423)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444444444333

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.

>PF09602 PhaP_Bmeg: Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg); InterPro: IPR011728 This entry describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium

Probab=83.08  E-value=43  Score=31.78  Aligned_cols=110  Identities=18%  Similarity=0.319  Sum_probs=58.9

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhh---------hHHHHH
Q psy10214         77 LEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHY---------DKIAVW  147 (415)
Q Consensus        77 ~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy---------~KIavW  147 (415)
                      -...+++..|-|.-+++|...|++ +.+   ..|.|.|-.-.++++....+++......-+.+..         +.|+.|
T Consensus        15 ~~~~~sls~~~~~~kqve~~~l~~-lkq---qqd~itk~veeLe~~~~q~~~~~s~~~~~~vk~L~k~~~~~l~d~inE~   90 (165)
T PF09602_consen   15 KQWSQSLSLFASFMKQVEQQTLKK-LKQ---QQDWITKQVEELEKELKQFKREFSDLYEEYVKQLRKATGNSLNDSINEW   90 (165)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHH-HHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345678899999999999999998 332   3455555544555555555555544443322222         256666


Q ss_pred             HHhHHhHHHHhhhhhcc-cc-cccccchhhHhHhHHHHHHHHHHHHH
Q psy10214        148 QNLLSDLQSCLQVLTKE-DE-VSTTLEKDEIKLEIDQATLKFLDLAR  192 (415)
Q Consensus       148 qnLlsdfQscLs~LSkq-E~-ser~~DqdEIKv~VEq~tnRFLD~AR  192 (415)
                      .+=...+-.-+..|... -. ++...  +-++-.++.++..||+..+
T Consensus        91 t~k~~El~~~i~el~~~~~Ks~~~~l--~q~~~~~eEtv~~~ieqqk  135 (165)
T PF09602_consen   91 TDKLNELSAKIQELLLSPSKSSFSLL--SQISKQYEETVKQLIEQQK  135 (165)
T ss_pred             HHHHHHHHHHHHHHHcchHHHHHHHH--HHHHhhHHHHHHHHHHHHH
Confidence            54333333333322111 00 00011  1234456777778888765

The role of the protein may include amino acid storage [].

>PHA02592 52 DNA topisomerase II medium subunit; Provisional

Probab=82.97  E-value=30  Score=36.78  Aligned_cols=121  Identities=9%  Similarity=0.053  Sum_probs=62.8

Q ss_pred             ChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHH
Q psy10214        108 KPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKF  187 (415)
Q Consensus       108 kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRF  187 (415)
                      -.+.|++||=.+|.++-..|++-.-+..     ..+++...+....+...++-+..   + ...+.+++.    ..+.+|
T Consensus       315 ~~~~Il~~f~~~R~~~~~kR~~~~l~k~-----~~r~~~l~~~~~fI~~vi~~~~~---~-~~~~~~~~~----~~l~~~  381 (439)
T PHA02592        315 NAEDLIRDFVEIRKTYVQKRIQYEIKET-----EEAFDLALAKAEFIKRVIAGEIV---L-QGKTRSELT----EELSDN  381 (439)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHh---c-cCCCHHHHH----HHHHHc
Confidence            6788999998888888877665443332     22333322222222222221111   1 001122222    122222


Q ss_pred             -HHHHHHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHh
Q psy10214        188 -LDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDK--IAVWQNLLSDLQ  250 (415)
Q Consensus       188 -LD~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eK--IeeWQsvL~dlq  250 (415)
                       +.  ..-=.|.|..++..       +.++++..|+.|++.++.-|+.+.++  .+-|..-|+++.
T Consensus       382 ~~~--~~q~~~lL~m~L~~-------LT~~e~~kL~~e~~~l~~ei~~l~~~t~~~~w~~DL~~~~  438 (439)
T PHA02592        382 KDF--GEYADKLVAMNIYS-------MTSDEREKLQKEAEELEKEHEYWKKTTAKKEYIKDLEELK  438 (439)
T ss_pred             CCC--HHHHHHHHHhHHHH-------hhHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence             10  11122444444333       66888888888888888877777665  555988888764

>KOG4552|consensus

Probab=82.97  E-value=40  Score=33.65  Aligned_cols=18  Identities=50%  Similarity=0.445  Sum_probs=16.4

Q ss_pred             HHHHHHHhhcChhHHHHh
Q psy10214         98 LQKRFLLSALKPELIVKE  115 (415)
Q Consensus        98 Lqkr~~ls~~kpe~i~ke  115 (415)
                      +++|++.++..-|.|+||
T Consensus         9 trerLL~~~dDlE~i~ke   26 (272)
T KOG4552|consen    9 TRERLLESADDLEHIVKE   26 (272)
T ss_pred             HHHHHHHHhhHHHHHHHH
Confidence            578999999999999999

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=82.95  E-value=37  Score=30.89  Aligned_cols=117  Identities=16%  Similarity=0.214  Sum_probs=66.4

Q ss_pred             hchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHH-HHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHH---H
Q psy10214        118 MVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQ-SCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLAR---Q  193 (415)
Q Consensus       118 ~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQ-scLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~AR---Q  193 (415)
                      ..+.++.++|-.......-|.+.-.++..++++-+.|. .-|..|               +..+.....++-+-..   .
T Consensus         3 ~k~~~i~~~Rl~~~~lk~~l~k~~~ql~~ke~lge~L~~iDFeqL---------------kien~~l~~kIeERn~eL~~   67 (177)
T PF13870_consen    3 QKRNEISKLRLKNITLKHQLAKLEEQLRQKEELGEGLHLIDFEQL---------------KIENQQLNEKIEERNKELLK   67 (177)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHH---------------HHHHHHHHHHHHHHHHHHHH
Confidence            34567888888887777777777777777776655554 333333               2222222212211110   1


Q ss_pred             HHHHHHHHHHhhhccCchh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        194 MEAFFLQKRFLLSALKPEL-IVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDL  249 (415)
Q Consensus       194 LE~FFLQKrlllSa~KPe~-vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dl  249 (415)
                      |-.-.-...+.++++|.+. .+..++..++.+|..++..+.+..+.+..-+..-..+
T Consensus        68 Lk~~~~~~v~~L~h~keKl~~~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~  124 (177)
T PF13870_consen   68 LKKKIGKTVQILTHVKEKLHFLSEELERLKQELKDREEELAKLREELYRVKKERDKL  124 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            1111112223455555544 5577888888888888888888888877755554444

>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=82.13  E-value=17  Score=32.53  Aligned_cols=106  Identities=21%  Similarity=0.316  Sum_probs=55.5

Q ss_pred             cchhHhhhhhhccccCCCCCCC-CCC-----------------CCchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy10214         44 LLQGPLAYLEKTTSNIGLPDGR-SLS-----------------PLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLS  105 (415)
Q Consensus        44 ~f~~~l~~~~~~~~~~~~~~~~-~~~-----------------~~~k~E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls  105 (415)
                      +|-+|+.+|........++... .+.                 ....++.+..++....-+|..||++|.       +.+
T Consensus        18 ~f~~si~~l~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~elA~dIi~kakqIe~-------LId   90 (144)
T PF11221_consen   18 QFCNSIGYLQRDAPPSPLSPNDPSISDPKPQAPPQQQQQAEPAPDPPEEFEENIKELATDIIRKAKQIEY-------LID   90 (144)
T ss_dssp             HHHHHHHHHHHTTGGGG-----------------------------HHHHHHHHHHHHHHHHHHHHHHHH-------HHH
T ss_pred             HHHHHHhhhccCCCCCCCCCCcccccCccccchhhhhhhhcccCCChhhHHHHHHHHHHHHHHHHHHHHH-------HHH
Confidence            4667777777664444443333 222                 235677777788777788999999984       455


Q ss_pred             hcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhh
Q psy10214        106 ALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVL  161 (415)
Q Consensus       106 ~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~L  161 (415)
                      .+=....-.|..  .+.|.+|..|+...++.+++-   +..=+++++.++.+|..+
T Consensus        91 sLPg~~~see~Q--~~~i~~L~~E~~~~~~el~~~---v~e~e~ll~~v~~~i~~i  141 (144)
T PF11221_consen   91 SLPGIEVSEEEQ--LKRIKELEEENEEAEEELQEA---VKEAEELLKQVQELIREI  141 (144)
T ss_dssp             HSTTSSS-HHHH--HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHTT
T ss_pred             hCCCCCCCHHHH--HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Confidence            554322222200  024555555555555444433   333345566777777665

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. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.

>KOG0977|consensus

Probab=82.05  E-value=45  Score=36.74  Aligned_cols=54  Identities=19%  Similarity=0.334  Sum_probs=42.3

Q ss_pred             ChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhh
Q psy10214        108 KPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVL  161 (415)
Q Consensus       108 kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~L  161 (415)
                      +-.-+..|+++.+.|+.++|+-+.++...+..+-+++..|...++.+++.+..+
T Consensus       107 ~ra~~e~ei~kl~~e~~elr~~~~~~~k~~~~~re~~~~~~~~l~~leAe~~~~  160 (546)
T KOG0977|consen  107 ERAKLEIEITKLREELKELRKKLEKAEKERRGAREKLDDYLSRLSELEAEINTL  160 (546)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhhhhhhhhHHHHH
Confidence            444566677778888888888888888888888889999998888888766644

>KOG0963|consensus

Probab=81.70  E-value=96  Score=34.84  Aligned_cols=57  Identities=21%  Similarity=0.204  Sum_probs=34.3

Q ss_pred             CCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcchhhHHhhc
Q psy10214        346 PSSGMMFMGPGGPRGGGNAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAYLEKTT  405 (415)
Q Consensus       346 ~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~le~~t  405 (415)
                      +-+--|++++.++.+|...-++|. +.++--+|=+.|+.--  +-+..+..++++|+-++
T Consensus       459 ~e~s~~~~~p~~~~~~~~s~~l~i-i~~qRdrfr~~n~~~e--~~~r~a~~~~~~l~~el  515 (629)
T KOG0963|consen  459 PESSIMGGGPSLPNGGVLSRILSV-ISSQRDRFRARNVELE--AQVRLANDKIGFLESEL  515 (629)
T ss_pred             CcccccCCCCCccccccccccchh-hhcccchhhhhhhhHH--HHHhhccCchhHHhhhh
Confidence            445567788888877777443332 2346666766666432  22345677777777654

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

Probab=81.63  E-value=43  Score=30.77  Aligned_cols=13  Identities=23%  Similarity=0.593  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHHH
Q psy10214        215 KEDIVDLRHDLAR  227 (415)
Q Consensus       215 KEEI~dLK~ELqR  227 (415)
                      ..+|.+|+.+|+.
T Consensus       137 ~~ei~~lr~~iE~  149 (177)
T PF07798_consen  137 DTEIANLRTEIES  149 (177)
T ss_pred             HHHHHHHHHHHHH
Confidence            4456666666553

>TIGR00634 recN DNA repair protein RecN

Probab=81.59  E-value=80  Score=33.86  Aligned_cols=27  Identities=15%  Similarity=0.197  Sum_probs=19.0

Q ss_pred             HHHhhhHHHHHHHhHHhHHHHhhhhhc
Q psy10214        137 IKRHYDKIAVWQNLLSDLQSCLQVLTK  163 (415)
Q Consensus       137 Lrkhy~KIavWqnLlsdfQscLs~LSk  163 (415)
                      |...|.++...+.+.++++.++..|..
T Consensus       214 L~~e~~~L~n~e~i~~~~~~~~~~L~~  240 (563)
T TIGR00634       214 LEAEQQRLSNLEKLRELSQNALAALRG  240 (563)
T ss_pred             HHHHHHHHhCHHHHHHHHHHHHHHHhC
Confidence            555555777777788888888777743

All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.

>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea

Probab=81.53  E-value=19  Score=29.18  Aligned_cols=35  Identities=23%  Similarity=0.317  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        215 KEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDL  249 (415)
Q Consensus       215 KEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dl  249 (415)
                      ++++..+..+|...+.-+....++++.|+..|..+
T Consensus        68 ~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~~  102 (106)
T PF01920_consen   68 EERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYEL  102 (106)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55666666677777777777777777777777654

Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.

>PRK12758 DNA topoisomerase IV subunit A; Provisional

Probab=81.03  E-value=36  Score=39.31  Aligned_cols=124  Identities=13%  Similarity=0.140  Sum_probs=69.6

Q ss_pred             cChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhh---HHHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHH
Q psy10214        107 LKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYD---KIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQA  183 (415)
Q Consensus       107 ~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~---KIavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~  183 (415)
                      +....|+++|=.++.++-..|.|...+++.=|-|+.   .|-+-+.....+.             .+.+.+++...+.  
T Consensus       328 ~~l~eiL~~~~~~r~~vl~rr~~~~l~k~~er~hi~~le~i~i~d~Ii~~Ir-------------~s~~~~~a~~~l~--  392 (869)
T PRK12758        328 LGVSDILRRSTDHTVSLLKQELEIRLSELEEQWHFASLEKIFIEERIYKEIE-------------EAETWEAVIEAID--  392 (869)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhhHHHHHHH-------------cCCCHHHHHHHHH--
Confidence            456789999999999999999888888877777772   2222111111111             1123334433332  


Q ss_pred             HHHH----------HH--HHHHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy10214        184 TLKF----------LD--LARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQ  250 (415)
Q Consensus       184 tnRF----------LD--~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq  250 (415)
                       .+|          +.  -+.++-.-=|+   ++|.+--+.+ .+|+.+|+.+|+..+.+|....+-|.+|-..|++-=
T Consensus       393 -~~~~p~~~~l~r~lte~qa~aIlemrL~---rlt~le~~k~-~~e~~~l~~~i~~~~~~L~~l~~~ii~el~~i~~ky  466 (869)
T PRK12758        393 -KGLEPFKKQFIREVTEDDIVRLTEIKIK---RISKFDSDKA-DELIARLEAEIAEVKHHLAHLTDYAIAYFTNLKKKY  466 (869)
T ss_pred             -HhcccchhhhcCCCCHHHHHHHHHhHHH---HHhchhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence             222          00  01111111111   2222223333 778999999999999999887776777766666553

>PF00521 DNA_topoisoIV: DNA gyrase/topoisomerase IV, subunit A; InterPro: IPR002205 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=81.02  E-value=13  Score=38.72  Aligned_cols=111  Identities=15%  Similarity=0.270  Sum_probs=56.6

Q ss_pred             cChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHH---HHhhhhhcccccccccchhhHhHhHHHH
Q psy10214        107 LKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQ---SCLQVLTKEDEVSTTLEKDEIKLEIDQA  183 (415)
Q Consensus       107 ~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQ---scLs~LSkqE~ser~~DqdEIKv~VEq~  183 (415)
                      ..++.|++||=.+|.++-..|.+..     |++-..+++.-..|+-++.   -++..+...      .+.++.+..+...
T Consensus       303 ~~~~eIL~~f~~~R~~~~~kR~~~~-----l~kl~~~l~il~gl~~~~~~idfIi~vI~~s------~~~~~~k~~L~~~  371 (426)
T PF00521_consen  303 DSLKEILKEFYEFRLEYYQKRKQYL-----LEKLEERLHILEGLIKALNKIDFIIEVIRGS------IDKNKAKKDLIEE  371 (426)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHS------SSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHhHHHHHHHHHHHHHHHhcc------ccchHHHHHHHhh
Confidence            4678999999888888777665544     4444444444443333332   111111110      0122222222211


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        184 TLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAV  241 (415)
Q Consensus       184 tnRFLD~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIee  241 (415)
                          |..  .-=.|.|.       .+--.+.++++.+|..|++.+++-|+.+.+.+..
T Consensus       372 ----L~~--~q~~yLL~-------m~L~~LT~~e~~kL~~e~~~l~~ei~~l~~~~~~  416 (426)
T PF00521_consen  372 ----LSE--EQADYLLS-------MPLRRLTKEEIEKLQKEIKELEKEIEELEKILPK  416 (426)
T ss_dssp             ----HCH--HHHHHHHT-------SBGGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             ----chH--HHHHHHHh-------chHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                111  00112332       2223467888888888888887777777766655

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA []. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication []. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB. This entry represents subunit A (gyrA and parC) of bacterial gyrase and topoisomerase IV, and the equivalent C-terminal region in eukaryotic topoisomerase II composed of a single polypeptide. This subunit has DNA-binding capacity. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome; PDB: 1ZVU_A 1AB4_A 1X75_A 3NUH_A 1BJT_A 1BGW_A 2RGR_A 3KSB_B 3FOE_B 2NOV_C ....

>COG3937 Uncharacterized conserved protein [Function unknown]

Probab=80.38  E-value=32  Score=30.72  Aligned_cols=99  Identities=12%  Similarity=0.123  Sum_probs=55.0

Q ss_pred             HHHHhhh-HHHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhhccCchhhh
Q psy10214        136 LIKRHYD-KIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIV  214 (415)
Q Consensus       136 LLrkhy~-KIavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFLQKrlllSa~KPe~vv  214 (415)
                      .|++.-. .+-.|..+.+..+.++..|++...+    +.+|.+.-|+-.++..-.....+|.= +++++..-.-+-+.+.
T Consensus         7 ~l~k~~~~gaG~~a~~~ek~~klvDelVkkGel----n~eEak~~vddl~~q~k~~~~e~e~K-~~r~i~~ml~~~~~~r   81 (108)
T COG3937           7 GLRKLALIGAGLAAETAEKVQKLVDELVKKGEL----NAEEAKRFVDDLLRQAKEAQGELEEK-IPRKIEEMLSDLEVAR   81 (108)
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHHHHHHcCCC----CHHHHHHHHHHHHHHHHHHhhhHHHh-hhHHHHHHHhhccccc
Confidence            3444333 5667888888888888888887665    67888777763332222211233332 2222222111222344


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        215 KEDIVDLRHDLARKEELIKRHYDKI  239 (415)
Q Consensus       215 KEEI~dLK~ELqRKErLIqKh~eKI  239 (415)
                      +.+.++|+.++++.++-+++..+++
T Consensus        82 ~~~~~~l~~rvd~Lerqv~~Lenk~  106 (108)
T COG3937          82 QSEMDELTERVDALERQVADLENKL  106 (108)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHh
Confidence            5556666666666666666665554

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=80.33  E-value=73  Score=35.56  Aligned_cols=19  Identities=32%  Similarity=0.434  Sum_probs=9.1

Q ss_pred             CCccCCCCCCCCCCCCCCC
Q psy10214        280 PGISAMGGPLPGMMGGMAP  298 (415)
Q Consensus       280 ~~~~~~~g~~~~~~~~map  298 (415)
                      ++.++++||.+|--+++++
T Consensus       381 ~~~~~~~~~~~~~~~~~~~  399 (624)
T PRK14959        381 PSGSAAEGPASGGAATIPT  399 (624)
T ss_pred             CCCCCCCCCCCCCCCCCCC
Confidence            3444556666643333433

>cd07666 BAR_SNX7 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7

Probab=80.17  E-value=65  Score=31.88  Aligned_cols=64  Identities=9%  Similarity=0.108  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHhhcChhHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhh
Q psy10214         90 ARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQ  159 (415)
Q Consensus        90 Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs  159 (415)
                      +-.+-++|-..|-.   .+|..--.|   .+.-+.+|..-|...+..+.|...+...+.+....|...+.
T Consensus        36 ~d~~~~~~s~~~~v---~~~~~eF~E---mkey~d~L~~~L~~ieki~~Rl~kr~~ey~~~~~~fgk~~~   99 (243)
T cd07666          36 GQTVKAVASSVRGV---KNRPEEFTE---MNEYVEAFSQKINVLDKISQRIYKEQREYFEELKEYGPIYT   99 (243)
T ss_pred             HHHHHHHHHhcccc---CCCCHHHHH---HHHHHHHHHHHhhhhHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            34555666654431   344333333   33366666666666665555444333233333333333333

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX7 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.

---

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	415
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-11
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-11
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-08
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	9e-08
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-08
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-07
3lbx_B	185	Beta-I spectrin, spectrin beta chain, erythrocyte;	5e-05
3fb2_A	218	Spectrin alpha chain, brain spectrin; non-erythroi	8e-05
1s35_A	214	Beta-I spectrin, spectrin beta chain, erythrocyte;	9e-05
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	9e-05
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	8e-04
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	3e-04
1u4q_A	322	Spectrin alpha chain, brain; alpha spectrin, three	6e-04
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	6e-04
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	7e-04

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 64.5 bits (156), Expect = 3e-11
 Identities = 22/134 (16%), Positives = 28/134 (20%), Gaps = 1/134 (0%)

Query: 257 AHQGSTSSASGTTPPNSTPTQSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQ 316
           +H                 T        M    P   G     +       +  M QQQ 
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61

Query: 317 QVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGG 376
               Q+Q+H Q  Q                     +M P  P   G              
Sbjct: 62  LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPN-AYMQPQVPVQMGTPLQQQQQPMAAPA 120

Query: 377 MGGPGNLGPGGMGP 390
            G P       M P
Sbjct: 121 YGQPSAAMGQNMRP 134

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 63.7 bits (154), Expect = 5e-11
 Identities = 31/156 (19%), Positives = 39/156 (25%), Gaps = 3/156 (1%)

Query: 259 QGSTSSASGTTPPNSTPTQSGPGISAMGGPLPGMMGGMAPIVPGSTMQPMSGMPQQQQ-- 316
           Q         TP         P   A  G   G MG        S  Q     P Q+Q  
Sbjct: 11  QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH 70

Query: 317 QVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGG 376
           Q   Q    M  M    +    P +         M       +    A     PSA  G 
Sbjct: 71  QQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQ 130

Query: 377 MGGPGNLGPGGMGPGGLLQGPLAYLEKTTSNIGLPD 412
              P N     +     L  P+  L      + +P 
Sbjct: 131 NMRPMN-QLYPIDLLTELPPPITDLTLPPPPLVIPP 165

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 54.1 bits (129), Expect = 6e-08
 Identities = 15/97 (15%), Positives = 20/97 (20%)

Query: 301 PGSTMQPMSGMPQQQQQVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRG 360
           P + +Q        QQ  Q                 G PP G         F+ P   + 
Sbjct: 10  PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69

Query: 361 GGNAGPPPFPSAGPGGMGGPGNLGPGGMGPGGLLQGP 397
                              P       M P   +Q  
Sbjct: 70  HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMG 106

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 53.3 bits (127), Expect = 9e-08
 Identities = 17/92 (18%), Positives = 24/92 (26%), Gaps = 2/92 (2%)

Query: 311 MPQQQQQV--QMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPP 368
           M   +++V  Q Q Q        Q      PP  P         MG        + G   
Sbjct: 1   MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ 60

Query: 369 FPSAGPGGMGGPGNLGPGGMGPGGLLQGPLAY 400
           F +     +    +     M    L   PL  
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVD 92

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 52.9 bits (126), Expect = 1e-07
 Identities = 16/124 (12%), Positives = 22/124 (17%), Gaps = 2/124 (1%)

Query: 250 QGWAKSPAHQGSTSSASGTTPPNSTPTQSGPGISAMGGPLPGMMGGMAPIVPGSTMQP-- 307
            G   +P  Q +                          P  G    + P       Q   
Sbjct: 16  YGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQ 75

Query: 308 MSGMPQQQQQVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPP 367
            +          +       +MQ Q     G P             G      G N  P 
Sbjct: 76  ATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPM 135

Query: 368 PFPS 371
               
Sbjct: 136 NQLY 139

>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 = 1e-08
 Identities = 41/270 (15%), Positives = 88/270 (32%), Gaps = 69/270 (25%)

Query: 43  GLLQGPLAYLEKTTSNIGLP-DGRSLSPLEKDEI--KLEIDQATLKFLD------LARQM 93
            LL   L YL+    +  LP +  + +P     I   +    AT           L   +
Sbjct: 305 SLL---LKYLDCRPQD--LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTII 359

Query: 94  EAFF-------LQKRFLLSALKPE--LIVKEV------NMVTKDIVDLRHDLARKEELIK 138
           E+          +K F   ++ P    I   +      +++  D++ + + L +   L++
Sbjct: 360 ESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS-LVE 418

Query: 139 RHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEK---------------DEIKLEIDQA 183
           +   +  +    +  +   L++  K +     L +               D I   +DQ 
Sbjct: 419 KQPKESTIS---IPSIY--LELKVKLEN-EYALHRSIVDHYNIPKTFDSDDLIPPYLDQY 472

Query: 184 T-------LKFLDLARQMEAF---FLQKRFLLSALK---PELIVKEDIVDLRHDLARKEE 230
                   LK ++   +M  F   FL  RFL   ++           I++    L    +
Sbjct: 473 FYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL----K 528

Query: 231 LIKRH-YDKIAVWQNLLSDLQGWAKSPAHQ 259
             K +  D    ++ L++ +  +       
Sbjct: 529 FYKPYICDNDPKYERLVNAILDFLPKIEEN 558

>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 = 53.7 bits (128), Expect = 7e-08
 Identities = 49/323 (15%), Positives = 84/323 (26%), Gaps = 102/323 (31%)

Query: 27  GMGGPG---------------NLGPGG-----MG----PGGLLQGPLAYLEKTTSN-IGL 61
           G+ G G                          +     P  +L+     L +   N    
Sbjct: 157 GVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSR 216

Query: 62  PDGRSLSPLEKDEIKLEID--------QATLKFLD---LARQMEAFFLQKRFLL------ 104
            D  S   L    I+ E+         +  L  L     A+   AF L  + LL      
Sbjct: 217 SDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQ 276

Query: 105 --SALKPELIVKEVNMV------TKD--------IVDLR-HDLARKE------------E 135
               L        +++       T D         +D R  DL R+             E
Sbjct: 277 VTDFLSAA-TTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE 335

Query: 136 LIKRHYDKIAVWQNLLSD-----LQSCLQVLTKEDEVSTTLEK-----DEIKLEIDQATL 185
            I+        W+++  D     ++S L VL +  E     ++           I    L
Sbjct: 336 SIRDGLATWDNWKHVNCDKLTTIIESSLNVL-EPAEYRKMFDRLSVFPPSAH--IPTILL 392

Query: 186 KFL------DLARQMEAFFLQKRFLLSALKPELIVKEDI-VDLRHDLARKEELIKR---H 235
             +           +     +   +    K   I    I ++L+  L  +  L +    H
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH 452

Query: 236 YDKIAVWQNLLSDLQGWAKSPAH 258
           Y       N+          P +
Sbjct: 453 Y-------NIPKTFDSDDLIPPY 468

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 49.3 bits (117), Expect = 6e-07
 Identities = 31/145 (21%), Positives = 40/145 (27%), Gaps = 2/145 (1%)

Query: 255 SPAHQGSTSSASGTTPPNSTPTQSGPGISAMGGPLPGMMGGMAPIVPGST--MQPMSGMP 312
           S   +G     +G           GPGI    G        M     G    ++ + G  
Sbjct: 79  SMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPS 138

Query: 313 QQQQQVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSA 372
           QQ    Q +  +            G P   P G       MG G P  G    PP     
Sbjct: 139 QQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPP 198

Query: 373 GPGGMGGPGNLGPGGMGPGGLLQGP 397
               MG P   G     P   ++ P
Sbjct: 199 MGPPMGIPPGRGTPMGMPPPGMRPP 223

>3lbx_B Beta-I spectrin, spectrin beta chain, erythrocyte; tetramer, complex, three-helix bundle, alpha helix repeat, helical linker, actin capping; 2.80A {Homo sapiens} Length = 185

 Score = 42.6 bits (100), Expect = 5e-05
 Identities = 29/177 (16%), Positives = 66/177 (37%), Gaps = 25/177 (14%)

Query: 85  KFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRHYDKI 144
           +F  +AR + ++       +   +    V  V ++ K    +  ++  + +      +  
Sbjct: 8   RFFSMARDLLSWMESIIRQIETQERPRDVSSVELLMKYHQGINAEIETRSKNFSACLELG 67

Query: 145 AVWQNLL-------SDLQSCLQVL-TKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEA 196
              ++LL        +++  LQ + ++  E++   E    +L +     +F   A   EA
Sbjct: 68  ---ESLLQRQHQASEEIREKLQQVMSRRKEMNEKWEARWERLRMLLEVCQFSRDASVAEA 124

Query: 197 FFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYD---KIAVWQNLLSDLQ 250
           + + +   L++            D  H +   E+LIKRH       A W    + L+
Sbjct: 125 WLIAQEPYLASG-----------DFGHTVDSVEKLIKRHEAFEKSTASWAERFAALE 170

>3fb2_A Spectrin alpha chain, brain spectrin; non-erythroid alpha chain alpha-II spectrin, fordrin alpha chain, sptan1, SPTA2_human, NESG, HR5563A; 2.30A {Homo sapiens} Length = 218

 Score = 42.6 bits (100), Expect = 8e-05
 Identities = 29/189 (15%), Positives = 59/189 (31%), Gaps = 43/189 (22%)

Query: 87  LDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKRH---YDK 143
              +  ++ F    R L+S +          + + ++     D+   E L++RH     +
Sbjct: 9   SHDSHDLQRFLSDFRDLMSWIN----GIRGLVSSDELAK---DVTGAEALLERHQEHRTE 61

Query: 144 IAVWQNLL------------------SDLQSCLQVL-TKEDEVSTTLEKDEIKLEIDQAT 184
           I                          +++  L +L  +  ++     +  + L+     
Sbjct: 62  IDARAGTFQAFEQFGQQLLAHGHYASPEIKQKLDILDQERADLEKAWVQRRMMLDQCLEL 121

Query: 185 LKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYD---KIAV 241
             F     Q E +   +   L+             D    L   E LIK+H D    I V
Sbjct: 122 QLFHRDCEQAENWMAAREAFLNT-----------EDKGDSLDSVEALIKKHEDFDKAINV 170

Query: 242 WQNLLSDLQ 250
            +  ++ LQ
Sbjct: 171 QEEKIAALQ 179

>1s35_A Beta-I spectrin, spectrin beta chain, erythrocyte; two repeats of spectrin, alpha helical linker region, 3- helix coiled-coils, beta spectrin; 2.40A {Homo sapiens} SCOP: a.7.1.1 a.7.1.1 Length = 214

 Score = 42.6 bits (100), Expect = 9e-05
 Identities = 22/178 (12%), Positives = 53/178 (29%), Gaps = 36/178 (20%)

Query: 85  KFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTKDIVDLRHDLARKEELIKR----- 139
            FL      +A+    +  +++      + E   + +    ++ ++   ++  +R     
Sbjct: 4   AFLQDLDDFQAWLSITQKAVASEDMPESLPEAEQLLQQHAGIKDEIDGHQDSYQRVKESG 63

Query: 140 -------HYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLAR 192
                     +  +    L  L       T  D +    E     L       +F   A+
Sbjct: 64  EKVIQGQTDPEYLLLGQRLEGLD------TGWDALGRMWESRSHTLAQCLGFQEFQKDAK 117

Query: 193 QMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQ 250
           Q EA    + + L+ L           +    L   E  I++        ++ L  ++
Sbjct: 118 QAEAILSNQEYTLAHL-----------EPPDSLEAAEAGIRKF-------EDFLGSME 157

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 42.8 bits (100), Expect = 9e-05
 Identities = 19/74 (25%), Positives = 23/74 (31%)

Query: 318 VQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPSAGPGGM 377
           V    +  +   + Q           G   +G            G  G   FP A PGG 
Sbjct: 144 VTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGD 203

Query: 378 GGPGNLGPGGMGPG 391
             PG  GPGG  P 
Sbjct: 204 RFPGPAGPGGPPPP 217

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 39.7 bits (92), Expect = 8e-04
 Identities = 26/79 (32%), Positives = 28/79 (35%), Gaps = 3/79 (3%)

Query: 312 PQQQQQVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPPFPS 371
            Q   Q +MQ +   Q  Q  G G  GPP   GG S      G  G      A P     
Sbjct: 149 KQFLSQFEMQSRKTTQSGQMSGEGKAGPP---GGSSRAAFPQGGRGRGRFPGAVPGGDRF 205

Query: 372 AGPGGMGGPGNLGPGGMGP 390
            GP G GGP    P G   
Sbjct: 206 PGPAGPGGPPPPFPAGQTH 224

>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* Length = 562

 Score = 41.8 bits (97), Expect = 3e-04
 Identities = 28/102 (27%), Positives = 39/102 (38%), Gaps = 9/102 (8%)

Query: 300 VPGSTMQPMSGMP----QQQQQVQMQQQIHMQHMQQQGM---GPGGPPSGPGGPSSGMMF 352
           +P   M+P+  +     + Q Q    +   +  M Q  M    PGG     GG +S    
Sbjct: 202 LPLIKMKPVPDLVPGNFKSQLQKVPPEWKALTDMPQMRMELERPGGNEITRGGSTSYGTG 261

Query: 353 MGPGGPRGGGNAGPPPFPSAGPG--GMGGPGNLGPGGMGPGG 392
                PR   +AG     S+GPG  G   PG+ G GG     
Sbjct: 262 SETESPRNPSSAGSWNSGSSGPGSTGNRNPGSSGTGGTATWK 303

>1u4q_A Spectrin alpha chain, brain; alpha spectrin, three repeats of spectrin, alpha-helical linker region, 3-helix coiled-coil, structural protein; 2.50A {Gallus gallus} SCOP: a.7.1.1 a.7.1.1 a.7.1.1 Length = 322

 Score = 40.6 bits (95), Expect = 6e-04
 Identities = 29/224 (12%), Positives = 75/224 (33%), Gaps = 48/224 (21%)

Query: 66  SLSPLEKDEIKLEIDQATLKFLDLA-------RQMEAFFLQKRFL--LSALKPELIVKEV 116
           + S  +  ++K + +    +F  +         ++       +F   +   +  +  K++
Sbjct: 71  TSSAFDTSQVKDKRETINGRFQRIKSMAAARRAKLNESHRLHQFFRDMDDEESWIKEKKL 130

Query: 117 NMVTKDIVDLRHDLARKEELIKRH---YDKIAVWQNLLSDLQSCLQVL------------ 161
            + ++D      DL   + L K+H     ++A  +  +  +    + L            
Sbjct: 131 LVSSEDYG---RDLTGVQNLRKKHKRLEAELAAHEPAIQGVLDTGKKLSDDNTIGKEEIQ 187

Query: 162 -------TKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIV 214
                      E+         +LE      +F+    + EA+  +K  L+++       
Sbjct: 188 QRLAQFVDHWKELKQLAAARGQRLEESLEYQQFVANVEEEEAWINEKMTLVAS------- 240

Query: 215 KEDIVDLRHDLARKEELIKRH---YDKIAVWQNLLSDLQGWAKS 255
                D    LA  + L+K+H        V ++ ++D+    + 
Sbjct: 241 ----EDYGDTLAAIQGLLKKHEAFETDFTVHKDRVNDVCANGED 280

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A Length = 504

 Score = 40.7 bits (96), Expect = 6e-04
 Identities = 14/91 (15%), Positives = 24/91 (26%), Gaps = 3/91 (3%)

Query: 309 SGMPQQQQQVQMQQQIHMQHMQQQGMGPGGPPSGPGGPSSGMMFMGPGGPRGGGNAGPPP 368
           SG+  +  Q  + Q      M ++  G  G   G     +          +       P 
Sbjct: 410 SGVSTRDVQELLTQYTKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPR 469

Query: 369 FPSAGPGGMGGPGNL--GPGGMGPGGLLQGP 397
                 GGM G  ++         G +    
Sbjct: 470 VL-HHMGGMAGLQSMMRQFQQGAAGNMKGMM 499

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	415
1ykh_A	108	RNA polymerase II mediator complex protein MED7; g	96.57
3vp9_A	92	General transcriptional corepressor TUP1; four hel	95.34
3iot_A	449	Maltose-binding protein, huntingtin fusion protei;	94.91
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	94.05
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	93.64
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	90.67
1s35_A	214	Beta-I spectrin, spectrin beta chain, erythrocyte;	89.97
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	87.88
1quu_A	250	Human skeletal muscle alpha-actinin 2; triple-heli	87.68
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	87.3
3fb2_A	218	Spectrin alpha chain, brain spectrin; non-erythroi	86.84
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	86.27
1hci_A	476	Alpha-actinin 2; triple-helix coiled coil, contrac	85.59
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	85.39
3lbx_B	185	Beta-I spectrin, spectrin beta chain, erythrocyte;	84.23
1xaw_A	140	Occludin; coiled-coil, cell adhesion; 1.45A {Homo	83.75
1fxk_A	107	Prefoldin; archaeal protein, chaperone; 2.30A {Met	82.49
2q12_A	265	DIP13 alpha, DCC-interacting protein 13 alpha; APP	82.25
1sjj_A	863	Actinin; 3-helix bundle, calponin homology domain,	82.08
1ykh_B	132	RNA polymerase II holoenzyme component SRB7; gene	81.99
1gmj_A	84	ATPase inhibitor; coiled-coil structure, P depende	81.82
3r6n_A	450	Desmoplakin; spectrin repeat, SH3 domain, cell adh	81.61
1u5p_A	216	Spectrin alpha chain, brain; alpha spectrin, two r	81.18

>1ykh_A RNA polymerase II mediator complex protein MED7; gene regulation; 3.00A {Saccharomyces cerevisiae} SCOP: a.252.1.2 PDB: 1yke_A

Probab=96.57  E-value=0.015  Score=49.71  Aligned_cols=56  Identities=16%  Similarity=0.194  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        192 RQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLS  247 (415)
Q Consensus       192 RQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~  247 (415)
                      ..+...|++.+++++.++|+++...-|..|+.++++|.+.++...+.++..+++|+
T Consensus        52 ~di~~lfiNmHhLlNeyRPhQARetL~~~le~Qi~~kr~e~~~i~~~~~~~~~~L~  107 (108)
T 1ykh_A           52 ENIRTILVNIHHLLNEYRPHQSRESLIMLLEEQLEYKRGEIREIEQVCKQVHDKLT  107 (108)
T ss_dssp             HHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            57888999999999999999999999999999999999999988888888877764

>3vp9_A General transcriptional corepressor TUP1; four helix bundle; 1.80A {Saccharomyces cerevisiae} PDB: 3vp8_A

Probab=95.34  E-value=0.0033  Score=52.46  Aligned_cols=79  Identities=15%  Similarity=0.219  Sum_probs=52.4

Q ss_pred             HHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHH
Q psy10214        148 QNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLAR  227 (415)
Q Consensus       148 qnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqR  227 (415)
                      .+|++++...|..++.+..++.....+|+...|...+    ....++..-++  .+..++.|.++.+.+||..||+||+.
T Consensus        13 ~ELLD~ir~Efe~~~~e~~~~k~q~~~eyE~ki~~Qi----~Emq~Ir~tvy--eLE~~h~kmKq~YEeEI~rLr~eLe~   86 (92)
T 3vp9_A           13 NELLDAIRQEFLQVSQEANTYRLQNQKDYDFKMNQQL----AEMQQIRNTVY--ERELTHRKMKDAYEEEIKHLKLGLEQ   86 (92)
T ss_dssp             ----CCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHH----HHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567777777777777655544454457766655555    66677777777  45678888899999999999999998


Q ss_pred             HHHHH
Q psy10214        228 KEELI  232 (415)
Q Consensus       228 KErLI  232 (415)
                      ++.-+
T Consensus        87 r~~q~   91 (92)
T 3vp9_A           87 RDHQI   91 (92)
T ss_dssp             -----
T ss_pred             cCCCC
Confidence            87644

>3iot_A Maltose-binding protein, huntingtin fusion protei; HTT-EX1, HD, sugar transport, transport, apoptos disease mutation, nucleus; 3.50A {Escherichia coli k-12} PDB: 3io6_A 3io4_A 3ior_A 3iou_A 3iov_A 3iow_A

Probab=94.91  E-value=0.0023  Score=61.52  Aligned_cols=8  Identities=13%  Similarity=0.322  Sum_probs=3.3

Q ss_pred             HHHHHHHH
Q psy10214         85 KFLDLARQ   92 (415)
Q Consensus        85 kFid~Arq   92 (415)
                      .|+++|+.
T Consensus       131 el~~~a~~  138 (449)
T 3iot_A          131 EIPALDKE  138 (449)
T ss_dssp             GHHHHHHH
T ss_pred             HHHHHHHH
Confidence            44444443

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=94.05  E-value=3.4  Score=40.49  Aligned_cols=39  Identities=18%  Similarity=0.068  Sum_probs=35.9

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        211 ELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDL  249 (415)
Q Consensus       211 e~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dl  249 (415)
                      ...+.++|+.|+.|-+|-+.+|.+...+|++....++|+
T Consensus       437 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  475 (487)
T 3oja_A          437 WDMYQHKETQLAEENARLKKLNGEADLALASANATLQEL  475 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHhhhhhhhhhhhhhhhHhcccHHHHH
Confidence            346689999999999999999999999999999999998

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

Probab=93.64  E-value=1.2  Score=44.54  Aligned_cols=38  Identities=11%  Similarity=0.205  Sum_probs=33.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy10214        214 VKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       214 vKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~  251 (415)
                      +++++.+++..++...+.+++.++.++.|.+-++.++.
T Consensus       542 ~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~  579 (597)
T 3oja_B          542 LEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEA  579 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            46888899999999999999999999999999998865

>1s35_A Beta-I spectrin, spectrin beta chain, erythrocyte; two repeats of spectrin, alpha helical linker region, 3- helix coiled-coils, beta spectrin; 2.40A {Homo sapiens} SCOP: a.7.1.1 a.7.1.1

Probab=89.97  E-value=8.6  Score=32.97  Aligned_cols=115  Identities=14%  Similarity=0.185  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcC-------hhHHHHhhhhchhHHHHHHHHHHHHH----HHHHHh-hhHHHHHHHhH
Q psy10214         84 LKFLDLARQMEAFFLQKRFLLSALK-------PELIVKEVNMVTKDIVDLRHDLARKE----ELIKRH-YDKIAVWQNLL  151 (415)
Q Consensus        84 ~kFid~Arq~E~fFLqkr~~ls~~k-------pe~i~ke~n~~~~di~eLR~ElaRKn----aLLrkh-y~KIavWqnLl  151 (415)
                      ++|..-++.+++|.-.+.-.|+...       .+.+++..+.+..||......+....    .|+... |.-...+...+
T Consensus         3 q~F~~~~~~l~~Wl~~~~~~l~~~~~~~dl~~v~~ll~~h~~~~~ei~~~~~~~~~~~~~g~~L~~~~~~~~~~~i~~~l   82 (214)
T 1s35_A            3 QAFLQDLDDFQAWLSITQKAVASEDMPESLPEAEQLLQQHAGIKDEIDGHQDSYQRVKESGEKVIQGQTDPEYLLLGQRL   82 (214)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHCCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCCCccHHHHHHHH
Confidence            5899999999999988888776532       24555555555555555444333322    333332 22223333344


Q ss_pred             HhHHHHhhhhhcccccccccchhhHhHhHH--HHHHHHHHHHHHHHHHHHHHHHhhh
Q psy10214        152 SDLQSCLQVLTKEDEVSTTLEKDEIKLEID--QATLKFLDLARQMEAFFLQKRFLLS  206 (415)
Q Consensus       152 sdfQscLs~LSkqE~ser~~DqdEIKv~VE--q~tnRFLD~ARQLE~FFLQKrlllS  206 (415)
                      +.+...-..|..-.        .+-+..++  .....|...+..++.+.-.+...++
T Consensus        83 ~~L~~~w~~L~~~~--------~~r~~~L~~~l~l~~F~~~~~~~~~Wl~~~E~~l~  131 (214)
T 1s35_A           83 EGLDTGWDALGRMW--------ESRSHTLAQCLGFQEFQKDAKQAEAILSNQEYTLA  131 (214)
T ss_dssp             HHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44443333331110        00111111  1245677777777777666655554

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

Probab=87.88  E-value=17  Score=33.63  Aligned_cols=23  Identities=17%  Similarity=0.398  Sum_probs=8.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHH
Q psy10214        122 DIVDLRHDLARKEELIKRHYDKI  144 (415)
Q Consensus       122 di~eLR~ElaRKnaLLrkhy~KI  144 (415)
                      ++.+++.++.+++.-|...-.||
T Consensus        54 ~l~d~~~~~~~~e~~i~~~~~ri   76 (256)
T 3na7_A           54 EKLALKLQVSKNEQTLQDTNAKI   76 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333

>1quu_A Human skeletal muscle alpha-actinin 2; triple-helix coiled coil, contractIle protein; 2.50A {Homo sapiens} SCOP: a.7.1.1 a.7.1.1

Probab=87.68  E-value=15  Score=32.79  Aligned_cols=121  Identities=17%  Similarity=0.202  Sum_probs=71.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCh--------hHHHHhhhhchhHHHHHHHHHHHHH----HHHHHhhhH--
Q psy10214         78 EIDQATLKFLDLARQMEAFFLQKRFLLSALKP--------ELIVKEVNMVTKDIVDLRHDLARKE----ELIKRHYDK--  143 (415)
Q Consensus        78 ~veq~~~kFid~Arq~E~fFLqkr~~ls~~kp--------e~i~ke~n~~~~di~eLR~ElaRKn----aLLrkhy~K--  143 (415)
                      .+|+...+|...|..+|+|.-.+.-.|+..-+        +.++|....|..|+......+....    +|+...|.-  
T Consensus        11 kLe~l~~~F~~~~~e~~~Wl~e~e~~l~~~~~~g~dl~~v~~llkkh~~~~~el~~~~~~v~~l~~~~~~L~~~~~~~~~   90 (250)
T 1quu_A           11 RLEHLAEKFRQKASTHETWAYGKEQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAV   90 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTHHHHHHCCCCSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcchh
Confidence            46777899999999999999888777774332        3344554555556555555444332    455544431  


Q ss_pred             ---------HHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy10214        144 ---------IAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSA  207 (415)
Q Consensus       144 ---------IavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFLQKrlllSa  207 (415)
                               ...|++|.+.....-..|         .+.-+..-.+|.....|...+..++.|.-.+...++.
T Consensus        91 ~I~~r~~~l~~~W~~L~~~~~~R~~~L---------~~~l~~~~~~d~l~~qF~~~a~~~~~Wl~~~e~~l~~  154 (250)
T 1quu_A           91 NVNDRCQKICDQWDRLGTLTQKRREAL---------ERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQD  154 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhcc
Confidence                     223444333333222222         1122223335555568888888999999887766654

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

Probab=87.30  E-value=41  Score=42.17  Aligned_cols=42  Identities=10%  Similarity=0.241  Sum_probs=31.1

Q ss_pred             chhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy10214        210 PELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       210 Pe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~  251 (415)
                      .++.++.+++..+..|+|-++||...-..-..|...+++++.
T Consensus      2057 ek~~L~~e~~~~~~kl~rA~~Li~gL~~Ek~RW~~~~~~l~~ 2098 (3245)
T 3vkg_A         2057 ETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQSENFNT 2098 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhccccHHHHHHHHHH
Confidence            334556777777777777788888888888889888888753

>3fb2_A Spectrin alpha chain, brain spectrin; non-erythroid alpha chain alpha-II spectrin, fordrin alpha chain, sptan1, SPTA2_human, NESG, HR5563A; 2.30A {Homo sapiens}

Probab=86.84  E-value=15  Score=31.97  Aligned_cols=44  Identities=18%  Similarity=0.163  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhc-------ChhHHHHhhhhchhHHHH
Q psy10214         82 ATLKFLDLARQMEAFFLQKRFLLSAL-------KPELIVKEVNMVTKDIVD  125 (415)
Q Consensus        82 ~~~kFid~Arq~E~fFLqkr~~ls~~-------kpe~i~ke~n~~~~di~e  125 (415)
                      ...+|+.-++.+.+|.-.+.-.|+..       ..|.++++.+.+.+||..
T Consensus        14 ~~~~F~~~~~~l~~Wl~~~~~~l~~~e~~~d~~~ve~ll~~H~~l~~ei~~   64 (218)
T 3fb2_A           14 DLQRFLSDFRDLMSWINGIRGLVSSDELAKDVTGAEALLERHQEHRTEIDA   64 (218)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCCCCSSSHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            46799999999999999998888642       234555655555555554

>2zqm_A Prefoldin beta subunit 1; chaperone; HET: CIT; 1.90A {Thermococcus SP} PDB: 2zdi_A

Probab=86.27  E-value=8.2  Score=31.03  Aligned_cols=37  Identities=22%  Similarity=0.167  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy10214        215 KEDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQG  251 (415)
Q Consensus       215 KEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL~dlq~  251 (415)
                      ++.+..+..+|++.+.-+....+++++|+..|..+.+
T Consensus        76 ~~~~e~ie~~i~~le~~~~~l~~~l~~lk~~l~~~~~  112 (117)
T 2zqm_A           76 KEKIETLEVRLNALERQEKKLNEKLKELTAQIQSALR  112 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            4445555666677777777888888888888888763

>1hci_A Alpha-actinin 2; triple-helix coiled coil, contractIle protein, muscle, Z- LINE, actin-binding protein; 2.8A {Homo sapiens} SCOP: a.7.1.1 a.7.1.1 a.7.1.1 a.7.1.1

Probab=85.59  E-value=26  Score=33.63  Aligned_cols=120  Identities=18%  Similarity=0.214  Sum_probs=66.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhcCh--------hHHHHhhhhchhHHHHHHHHHHHHH----HHHHHhhhH---
Q psy10214         79 IDQATLKFLDLARQMEAFFLQKRFLLSALKP--------ELIVKEVNMVTKDIVDLRHDLARKE----ELIKRHYDK---  143 (415)
Q Consensus        79 veq~~~kFid~Arq~E~fFLqkr~~ls~~kp--------e~i~ke~n~~~~di~eLR~ElaRKn----aLLrkhy~K---  143 (415)
                      ++++..+|..-|..+++|.-.+.-.|+..-.        +.++++...|..||......+..-.    .|+...|.-   
T Consensus       129 Le~~~~~f~~~~~~~~~Wl~e~e~~l~~~~~~g~dl~~v~~ll~kh~~~~~~l~~~~~~v~~l~~~~~~L~~~~~~~~~~  208 (476)
T 1hci_A          129 LEHLAEKFRQKASTHETWAYGKEQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVN  208 (476)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTHHHHHHCCGGGSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTTHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCccCCCHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhCcCcchhH
Confidence            4566789999999999999888887754322        3445555666666666665555443    444433321   


Q ss_pred             --------HHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy10214        144 --------IAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSA  207 (415)
Q Consensus       144 --------IavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFLQKrlllSa  207 (415)
                              ...|+.|.+.+...-..|...         -...-.++.....|...+..+..|+-.+...++.
T Consensus       209 I~~~~~~l~~~W~~L~~~~~~R~~~L~~~---------~~~~~~~e~l~~~f~~~a~~~~~Wl~~~~~~l~~  271 (476)
T 1hci_A          209 VNDRCQKICDQWDRLGTLTQKRREALERM---------EKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQD  271 (476)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence                    224544444444333333110         1111122333345777777777776655555443

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

Probab=85.39  E-value=50  Score=41.46  Aligned_cols=54  Identities=24%  Similarity=0.303  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcChhHH--HHhhhhchhHHHHHHHHHHHHHHHHHH
Q psy10214         86 FLDLARQMEAFFLQKRFLLSALKPELI--VKEVNMVTKDIVDLRHDLARKEELIKR  139 (415)
Q Consensus        86 Fid~Arq~E~fFLqkr~~ls~~kpe~i--~ke~n~~~~di~eLR~ElaRKnaLLrk  139 (415)
                      |||+-+.--.-+.+||-.+...+--+-  +.--+.++.+++++++||+.|+..|.+
T Consensus      1897 yLeli~~y~~ll~~K~~el~~~~~rl~~GL~KL~et~~~V~~l~~~L~~~~~~L~~ 1952 (3245)
T 3vkg_A         1897 YLDFINQVVLLINEKRDQLEEEQLHLNIGLKKLRDTEAQVKDLQVSLAQKNRELDV 1952 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777777777778888877765543221  111133555777777777777654443

>3lbx_B Beta-I spectrin, spectrin beta chain, erythrocyte; tetramer, complex, three-helix bundle, alpha helix repeat, helical linker, actin capping; 2.80A {Homo sapiens}

Probab=84.23  E-value=19  Score=30.83  Aligned_cols=149  Identities=14%  Similarity=0.160  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhc-------ChhHHHHhhhhchhHHHHHHHHHHHH----HHHHHHhhhHHHHHHHhH
Q psy10214         83 TLKFLDLARQMEAFFLQKRFLLSAL-------KPELIVKEVNMVTKDIVDLRHDLARK----EELIKRHYDKIAVWQNLL  151 (415)
Q Consensus        83 ~~kFid~Arq~E~fFLqkr~~ls~~-------kpe~i~ke~n~~~~di~eLR~ElaRK----naLLrkhy~KIavWqnLl  151 (415)
                      ..+|+.-++.+++|.-.+.-.++..       ..+.+++..+.+..+|...+..+..-    +.||...+.-...+...+
T Consensus         6 l~~F~~~~~dl~~Wl~~~~~~l~~~e~~~d~~~~e~ll~~H~~~~~ei~~~~~~~~~l~~~G~~L~~~~~~~~~~i~~~l   85 (185)
T 3lbx_B            6 KFRFFSMARDLLSWMESIIRQIETQERPRDVSSVELLMKYHQGINAEIETRSKNFSACLELGESLLQRQHQASEEIREKL   85 (185)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSCC--CCSSSCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCcCCCCHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCCCcHHHHHHHH
Confidence            4699999999999999888877653       33456666666666665554444333    355554332223334444


Q ss_pred             HhHHHHhhhhhcccccccccchhhHhHhHH--HHHHHHHHHHHHHHHHHHHHHHhhhccC-chhhhHHHHHHHHHHHHHH
Q psy10214        152 SDLQSCLQVLTKEDEVSTTLEKDEIKLEID--QATLKFLDLARQMEAFFLQKRFLLSALK-PELIVKEDIVDLRHDLARK  228 (415)
Q Consensus       152 sdfQscLs~LSkqE~ser~~DqdEIKv~VE--q~tnRFLD~ARQLE~FFLQKrlllSa~K-Pe~vvKEEI~dLK~ELqRK  228 (415)
                      +.+...-..|..-      .+  +-+..++  -....|..-+.+++.+.-.+...++..- ...  -.++..|-.+.+.-
T Consensus        86 ~~L~~~w~~L~~~------w~--~r~~~L~~~l~l~~F~~d~~~~~~Wl~~~e~~L~~~~~g~s--l~~ve~LlkkH~~f  155 (185)
T 3lbx_B           86 QQVMSRRKEMNEK------WE--ARWERLRMLLEVCQFSRDASVAEAWLIAQEPYLASGDFGHT--VDSVEKLIKRHEAF  155 (185)
T ss_dssp             HHHHHHHHHHHHH------HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCSS--HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH------HH--HHHHHHHHHHHHHHHHHhHHHHHHHHHHhHhhhccCCCCCC--HHHHHHHHHHHHHH
Confidence            4444333332111      00  0111111  1245677777888888776665554321 121  23455565555555


Q ss_pred             HHHHHHHHHHHHH
Q psy10214        229 EELIKRHYDKIAV  241 (415)
Q Consensus       229 ErLIqKh~eKIee  241 (415)
                      +..|..+.+||..
T Consensus       156 e~~l~~~~e~i~~  168 (185)
T 3lbx_B          156 EKSTASWAERFAA  168 (185)
T ss_dssp             HHHHHHTHHHHHH
T ss_pred             HHHHHHhHHHHHH
Confidence            5666666666554

>1xaw_A Occludin; coiled-coil, cell adhesion; 1.45A {Homo sapiens} SCOP: h.4.17.1 PDB: 1wpa_A 3g7c_A

Probab=83.75  E-value=3.2  Score=36.86  Aligned_cols=69  Identities=7%  Similarity=0.158  Sum_probs=37.8

Q ss_pred             hHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChhHHHHhhhhchh-----HHHHHHHHHHHHHHHHHHhhhHHHHHH
Q psy10214         74 EIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALKPELIVKEVNMVTK-----DIVDLRHDLARKEELIKRHYDKIAVWQ  148 (415)
Q Consensus        74 E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~kpe~i~ke~n~~~~-----di~eLR~ElaRKnaLLrkhy~KIavWq  148 (415)
                      |++.+|+.+..+|.+|-++|...  .    -....-..|+.|||.+.+     +..+-|+.+.-....|....-.|..|+
T Consensus        63 ~Lhaev~~v~~~F~~Ld~~L~~l--~----~~s~e~~~i~~EY~r~k~~K~dp~y~ekK~Rc~yL~~KLsHIK~lI~~YD  136 (140)
T 1xaw_A           63 SLQSVLDEINKELSRLDKELDDY--R----EESEEYMAAADEYNRLKQVKGSADYKSKKNHCKQLKSKLSHIKKMVGDYD  136 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHS--C----TTSHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhC--C----CCCHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            56778888888888888887651  1    111122357889988643     223333333333344444444455444

>1fxk_A Prefoldin; archaeal protein, chaperone; 2.30A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: a.2.5.1 PDB: 1fxk_B

Probab=82.49  E-value=13  Score=29.46  Aligned_cols=33  Identities=6%  Similarity=0.037  Sum_probs=23.1

Q ss_pred             hHHHHhhhhchhHHHHHHHHHHHHHHHHHHhhh
Q psy10214        110 ELIVKEVNMVTKDIVDLRHDLARKEELIKRHYD  142 (415)
Q Consensus       110 e~i~ke~n~~~~di~eLR~ElaRKnaLLrkhy~  142 (415)
                      +.++.+|+.+..++..+..++..++.-++++..
T Consensus         4 Q~~i~~f~~lq~~~~~l~~q~~~l~~~~~e~~~   36 (107)
T 1fxk_A            4 QHQLAQFQQLQQQAQAISVQKQTVEMQINETQK   36 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666777777777777777777776666554

>2q12_A DIP13 alpha, DCC-interacting protein 13 alpha; APPL1, BAR domain, protein transport; 1.79A {Homo sapiens} PDB: 2z0n_A

Probab=82.25  E-value=29  Score=31.53  Aligned_cols=21  Identities=5%  Similarity=0.099  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q psy10214         80 DQATLKFLDLARQMEAFFLQK  100 (415)
Q Consensus        80 eq~~~kFid~Arq~E~fFLqk  100 (415)
                      -.++.+|.++.+.+++|...-
T Consensus        83 ~~~L~~f~~~l~ei~~~~~~l  103 (265)
T 2q12_A           83 SSTLQQFSKVIDELSSCHAVL  103 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            478899999999999987543

>1sjj_A Actinin; 3-helix bundle, calponin homology domain, calmodulin-like domain, actin binding protein, contractIle protein; 20.00A {Gallus gallus} SCOP: i.15.1.1

Probab=82.08  E-value=19  Score=37.73  Aligned_cols=29  Identities=24%  Similarity=0.211  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy10214         79 IDQATLKFLDLARQMEAFFLQKRFLLSAL  107 (415)
Q Consensus        79 veq~~~kFid~Arq~E~fFLqkr~~ls~~  107 (415)
                      +++...+|...|..+|+|...+.-.|+..
T Consensus       368 Le~l~~~F~~~~~~~~~Wl~~~e~~l~~~  396 (863)
T 1sjj_A          368 LDHLAEKFRQKASIHESWTDGKEAMLQQK  396 (863)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            44567889999999999998888877764

>1ykh_B RNA polymerase II holoenzyme component SRB7; gene regulation; 3.00A {Saccharomyces cerevisiae} SCOP: a.252.1.1

Probab=81.99  E-value=12  Score=32.17  Aligned_cols=103  Identities=17%  Similarity=0.185  Sum_probs=57.5

Q ss_pred             cchhHhhhhhhccccCCCCC-CCC-----CCCCchhhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC----hhHHH
Q psy10214         44 LLQGPLAYLEKTTSNIGLPD-GRS-----LSPLEKDEIKLEIDQATLKFLDLARQMEAFFLQKRFLLSALK----PELIV  113 (415)
Q Consensus        44 ~f~~~l~~~~~~~~~~~~~~-~~~-----~~~~~k~E~~~~veq~~~kFid~Arq~E~fFLqkr~~ls~~k----pe~i~  113 (415)
                      .|-+|+.+|...-...-+.. .+.     ....+.++....++....-+|..||++|.       +.+.+=    .|.--
T Consensus        18 ~f~nsig~Lq~~a~p~~~~~~~~~~~~~~~~~~~~~~f~~~~~ela~dli~k~kqIe~-------LIdsLP~~~~see~Q   90 (132)
T 1ykh_B           18 QFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDELSTDIILKTRQINK-------LIDSLPGVDVSAEEQ   90 (132)
T ss_dssp             HHHHHHHHHHHSSCCC---------------CCCHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHSTTTTCCHHHH
T ss_pred             HHHHHHHHHhcCCCcccCCCCCCCCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-------HHHhCCCCCCCHHHH
Confidence            46677777776543333322 111     22345678888888888889999999993       333332    22222


Q ss_pred             HhhhhchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhhh
Q psy10214        114 KEVNMVTKDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLT  162 (415)
Q Consensus       114 ke~n~~~~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~LS  162 (415)
                      .+      .|.+|.+|+...++.+++--.   .=+.+++.++.+|..++
T Consensus        91 ~~------ri~~L~~E~~~~~~el~~~v~---e~e~ll~~v~~~l~~i~  130 (132)
T 1ykh_B           91 LR------KIDMLQKKLVEVEDEKIEAIK---KKEKLMRHVDSMIEDFV  130 (132)
T ss_dssp             HH------HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHTTC
T ss_pred             HH------HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHh
Confidence            22      555666666666554444333   33455677777776653

>1gmj_A ATPase inhibitor; coiled-coil structure, P dependent oligomerization, ATP hydrolysis; 2.2A {Bos taurus} SCOP: h.4.8.1 PDB: 1ohh_H* 1hf9_A

Probab=81.82  E-value=9.7  Score=31.35  Aligned_cols=55  Identities=18%  Similarity=0.299  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhccCchhhhHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy10214        185 LKFLDLARQMEAFFLQKRFLLSALKPELIVKEDIVDLR----HDLARKEELIKRHYDKIAVWQNLLSDLQ  250 (415)
Q Consensus       185 nRFLD~ARQLE~FFLQKrlllSa~KPe~vvKEEI~dLK----~ELqRKErLIqKh~eKIeeWQsvL~dlq  250 (415)
                      ..|-..-.+.|.+|+.++.           ++.+..|+    .||+....-|++|.+.|+.++.-++.|.
T Consensus        20 gaFgKrEaA~Ee~Yfrqke-----------kEqL~~LKkkl~~el~~h~~ei~~le~~i~rhk~~i~~l~   78 (84)
T 1gmj_A           20 GAFGKREQAEEERYFRARA-----------KEQLAALKKHKENEISHHAKEIERLQKEIERHKQSIKKLK   78 (84)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcccHHHHhHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4566666777776553332           22222233    4455555555555555555555555553

>3r6n_A Desmoplakin; spectrin repeat, SH3 domain, cell adhesion, desmosome; 2.95A {Homo sapiens}

Probab=81.61  E-value=48  Score=33.59  Aligned_cols=31  Identities=26%  Similarity=0.247  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHH---HHHHHHHHHHHHHhcccC
Q psy10214        224 DLARKEELIKRHY---DKIAVWQNLLSDLQGWAK  254 (415)
Q Consensus       224 ELqRKErLIqKh~---eKIeeWQsvL~dlq~~~~  254 (415)
                      .+..-+.||++|.   +.|+.+...++.|...+.
T Consensus       233 d~~~~e~LLkkh~~le~~l~~~~~~I~~L~~qA~  266 (450)
T 3r6n_A          233 PLQHLLEQIKELEKEREKILEYKRQVQNLVNKSK  266 (450)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444456666665   577888888888866455

>1u5p_A Spectrin alpha chain, brain; alpha spectrin, two repeats of spectrin, alpha-helical linker region, 3-helix coiled coil, structural protein; 2.00A {Gallus gallus} SCOP: a.7.1.1 a.7.1.1

Probab=81.18  E-value=25  Score=30.06  Aligned_cols=23  Identities=13%  Similarity=0.225  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhh
Q psy10214         84 LKFLDLARQMEAFFLQKRFLLSA  106 (415)
Q Consensus        84 ~kFid~Arq~E~fFLqkr~~ls~  106 (415)
                      .+|.+.+..+++|.-.+.-.|+.
T Consensus         6 ~~F~~~~~~l~~Wl~~~e~~l~~   28 (216)
T 1u5p_A            6 QNFNTGIKDFDFWLSEVEALLAS   28 (216)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcC
Confidence            58999999999998888777754

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	415
d1ykha1	95	RNA polymerase II mediator complex protein MED7 {B	96.38
d2elba1	268	DCC-interacting protein 13-alpha, APPL1 {Human (Ho	89.75

>d1ykha1 a.252.1.2 (A:111-205) RNA polymerase II mediator complex protein MED7 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: Mediator hinge subcomplex-like
superfamily: Mediator hinge subcomplex-like
family: MED7 hinge region
domain: RNA polymerase II mediator complex protein MED7
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.38  E-value=0.019  Score=46.03  Aligned_cols=55  Identities=16%  Similarity=0.188  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHHhhhccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10214        192 RQMEAFFLQKRFLLSALKPELIVKEDIVDLRHDLARKEELIKRHYDKIAVWQNLL  246 (415)
Q Consensus       192 RQLE~FFLQKrlllSa~KPe~vvKEEI~dLK~ELqRKErLIqKh~eKIeeWQsvL  246 (415)
                      ..+...|++.+++++.++|+++...-|..++.++++|.+.++...+.++.-+..|
T Consensus        39 edl~~LfiN~HhllNeyRPhQAResLi~lme~Ql~~kr~~~~~i~~~~~~~~~~L   93 (95)
T d1ykha1          39 ENIRTILVNIHHLLNEYRPHQSRESLIMLLEEQLEYKRGEIREIEQVCKQVHDKL   93 (95)
T ss_dssp             HHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccCcHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4678899999999999999999999999999999999999888887777766655

>d2elba1 a.238.1.1 (A:6-273) DCC-interacting protein 13-alpha, APPL1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: BAR/IMD domain-like
superfamily: BAR/IMD domain-like
family: BAR domain
domain: DCC-interacting protein 13-alpha, APPL1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.75  E-value=4.2  Score=34.52  Aligned_cols=74  Identities=9%  Similarity=0.096  Sum_probs=35.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhhHHHHHHHhHHhHHHHhhhhhcccccccccchhhHhHhHHHHHHHHHHHHHHHHHHHH
Q psy10214        121 KDIVDLRHDLARKEELIKRHYDKIAVWQNLLSDLQSCLQVLTKEDEVSTTLEKDEIKLEIDQATLKFLDLARQMEAFFL  199 (415)
Q Consensus       121 ~di~eLR~ElaRKnaLLrkhy~KIavWqnLlsdfQscLs~LSkqE~ser~~DqdEIKv~VEq~tnRFLD~ARQLE~FFL  199 (415)
                      +++..++.-+.+.-...++.++...........|-.+|..+...... .+.|.+.+    ..++.+|.+..+.+..++.
T Consensus        23 ~~~~~l~~~l~kl~k~~~~~~~~~~~~~~~~~~f~~~L~~~~~~~~~-~~~dd~~~----~~~l~~f~~~~~el~~~~~   96 (268)
T d2elba1          23 EDATAISNYMNQLYQAMHRIYDAQNELSAATHLTSKLLKEYEKQRFP-LGGDDEVM----SSTLQQFSKVIDELSSCHA   96 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGSCCC------CHH----HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccc-ccCCcHHH----HHHHHHHHHHHHHHHHHHH
Confidence            35555555555544444444444444444444555555555433211 23343333    4555677777777766553