<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Detailed information on MDP03996

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMAQTTGPFASHARSASIANSPSAHRRAGGGVGPAQHASPSNNPSFPRPFANAAFPGTVSAPRSAAAPNSALAPPKSIQHLSLLTTHTPTSIAKLAFPPHTTVFWHRLQKICDDAASTAGHDHQRQDAATSSTTASAGSSQELNKAWDNGVQRLLSSLHPSRLRTHAIDESHRKDCTAFQLLLKDPLIYTISKGHPSGNNAPSASGTSEAELWVFVVVTDQEELRDKDTSDSDVEAVETGAAHPGNRDAAAGESAQVTTRGDSTLLDLTLARHLSADLAKSLARLSTSAHATSGSYRLSAAATNSIDGKGKQSSLTSQQRQAHRRFMASLKAKIIDSFAGAQPPSSKHKRDRLRLRDSVVFLPTSQSGSRSTATPDASWFAAPGLHKASFSGVTNSPCLLTQLVISLTATSLFVHATSRPLAALPLIDTRHANTASSLASSPVRPTMLIAPLGSRVELMGIVPMSGIANEHLTELCQSFAVFNSASQHTEPNGQSPFAAGVAICAFSRPTSCPQSQQQEPHLQDPQQLTDASLIPSAQRGTSDQGMPLAATTGVADERANANARDEGLLQFLWPAAWCLVVQEQASTSTGALGLGSNAMNDLKSMQSQPLTPLKELVSFTLKVLNDANESALAQSTAPYAPGEPDEASIARHRADRMPSTRADITPASMSFADFDFAMPIASSATPSHALPTAGQSVPPGASPLKREPASTEPVQAANSTEAFGQDLNWMHFLSPQISDAAVSSSEPAFALQIDSTSMPAPTSGADPAVNATAMETDGAKHSHADQSGSNWLVSSGSSTAPEGGQTAAAQSSDPAASQSLLQPHPHLQSHGPTLLQGQQETSPLGFTHPTSSKRKPGEGDIFGNLGLLTEDDFSFFDESAFGLDPEGELPRHMEQPAETIRMGPSQHHLAYAQPRAVENHSTAPGPSMPAETRPASSIAAAVIDDVTMDDVGQSSLDALFSAIPGLQDAMVSSETSQAPTAPLQSSLAASTAVTQPAPSRLGHSAAQDLAVSAHAFHPAMSSFTPRDASGATPFGDPASLPGFTPSSLTESSPTFGHPHYKTPRTPCSPVEEYRDGATIVDLHNGHRMGESAQSYRDRNAASAPDLHAPDQHQLSGYKADSFLHDDQLHLADASTAAAAAANAAMDTDASSRKRPAIVPNAFLPLRLPEARKPLQKLAAGARTNLGRKYDSLGKFASRPKTATATATAKTTVLNASNATTTAEHPSSGNTGKGAERMDRQSFSETGRLGTRYPATRPSSSKMPSLRGEALLQLRRDRHGKSSPGLALNSLGRSSSSRVAEAPATPRSSDDVVLSGAMSASGSDTSGSEDDDSDDALSDSEATALTLSPQDQATLKDVSLDVVASYLCGASYVSRAHWPAGSSAAAEQTNEDPATLRSLVKPPLPFSRFTQTALIAGSTATSISSRPTLRRWMLSRTAAWLIENPQFRSMYGMLGIGSMASSELAIGDKIEVLETMASALSIAPVLTSTSEPAETSTASTSFEAEVALPKLRDLVRPSKHVAGVAADSVEVAEVLEPTRIAAGCQGSVVEALPSSLTLWDKSKLSAVSGQKHVVAKVLLTDASPAWHEEIVAWLERLRVTFETHGLGTHVSNAQSILAVADGSESLALSSCLDQFWQDGETWLDTLRSISSRVELDLLQGKHVVVYTLQPPNSAACASTGFRGLLRLEADLRAMVSEQVGVLAEQLLVRAVSPSMMTESGSLGFGQQSQTLRRLAFSVYDQLPRLVRRQPAKVLHGREAGPISAAVQFPSFSLSTASASGTCTAGQTNLSLSWPLEPAAALDEHVLLHVSYRVCQTGSREQAEQAGGTSRNDGSAPFVGANVFGLGGLADGDQAASTRTRERIVLVSAIDERGGSSTVDALAANDSESSIEACVERVWRFALAEASRARVRWRLAISSAVVMGQRELVAWQRMIGSYVASTRAEERVMGSVVLLSVRPDESGAVVAERGGRTKPSQPWAATAEKSSLVLLDAADFSQMVKFAEPMPMGWTQAVAESQMQHHQHASSRWGRVGQPGLGRRYAVQVVQIDSAAARECGRLDSEDRTQPTHLAAPTIPARTCRAKLGVTASAAMPVISAAKLASHIWRGAAQSAANAAHNSANTFRGAFQGASSGSTSSTGSSASGWASGLSSGGSSAGAGAGGAKFHAGRGAHFSYQHTGRALSQASTTSNSDSNNKSTDDDDEARRQKAYKLRLDGQHHYDRSMLASSPGHLTNSHMQVRFRHAFAAKQAPLLVTSSAQADTGDVSSHNQRHASTLAATPTTTEASAGAEAPLKVNTNTSAHDLVYRDLLYASKRRDAQQVRLSVDAFNALPKDQKTTAGFNMVMESLLSVRRSGQPVREITDTYNDMIQTGLAPNSRTYTALQLMSVAHSSRNWFDDEKAYNAVLSSCALRGDVDRALSVLDLLERSMFADTDAHTFKHLIRTFVTDPQLKPQETHQMQQSRKLAACKQVFDEFLLASQKPQWKHDLNRIVWCSLLEAHFALNDPAGAIKLFEKMLQGGDNVPALDSSIISAIIRGFLDIHDTDTALHWFAKVTSPEASSPSSLPIPTPQTTEYLLSHLAQSGGQYLEPLQRVFHVYLENCVERQVPAQISALIDLVSANVASAQRLLHAGSADQANASIDRALDAAAAFFAQEAGPLRRFKDGTKIRNTVHTVIQLSDILLAANRIVDAGSTLTYARLFLDKIDVTAAPHQQLGAQLSQLTNRILTAADPANDAKLNSIRLFVSAEYVAPVLRQADMLDEQVAASLASLYRSVHKQSPEALVDLPLSADAWTLILEAFCFEELNVRPLNLDAFKADGVPIVLHHLAELSAADASESAEGSVDRSSIDTSKAVEVTVTRYGQEALALLPEWARQNATSAEQQEAQESAAVRGEVSSDAGSVSQFSASTPATTPPQQHSPLHRQDLPAPALSAFYTGTATSAFSFPPVQVIDTDFGQELLSFARPSGQNEAPRLYAKALEETKVGNYAHPEGLAFLIGAFGRLGDVERVEEVYAMAQHVLHALVGDPNWQTNAWFVVEDNMIQALSHAGRSDAATVHRHRIIAAGGTPTPTSYAALIATIRDTTDDASIAQELFDESQRFQVRPTAYLFNTVISKLSRARKADRALQLFDEMTLNYRIKPTSVTYGAVINACTRIGDEQRAVHLFERMEHDPAFKPRVPPYNTMMQYYIQSVPDREKALVYYHKMRAAGVQPSAHTYKLLLDMYGAIAPVEPLEMERVFQELADNPSVAVQSTHWASLINCYGCMLNDLDRAIATFDSIASHPSSQMRKDGANLPNAVSFEALLADEAGRIADDGLRGQPADPRLLDGARRSWTQRGSCAV
Length3338
PositionKinase
OrganismSporisorium scitamineum
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Basidiomycota> Ustilaginomycotina> Ustilaginomycetes> Ustilaginales> Ustilaginaceae> Sporisorium.
Aromaticity0.06
Grand average of hydropathy-0.285
Instability index46.38
Isoelectric point6.06
Molecular weight355338.32
Publications









Function






Annotated function

Component of the SRB8-11 complex. The SRB8-11 complex is a
regulatory module of the Mediator complex which is itself involved in
regulation of basal and activated RNA polymerase II-dependent
transcription. The SRB8-11 complex may be involved in the
transcriptional repression of a subset of genes regulated by Mediator.
It may inhibit the association of the Mediator complex with RNA
polymerase II to form the holoenzyme complex.



GO - Cellular Component
mediator complex	GO:0016592	IEA:InterPro

GO - Biological Function
transcription coregulator activity	GO:0003712	IEA:InterPro

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IEA:InterPro









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP03996
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     112.46|      34|      37|    3090|    3126|       1
---------------------------------------------------------------------------
 3091- 3124 (56.76/30.03)	FDE.SQRFQVRPTAYLFNTVISKLSRARKADRALQ
 3126- 3160 (55.69/31.21)	FDEmTLNYRIKPTSVTYGAVINACTRIGDEQRAVH
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     146.45|      35|      37|    3253|    3289|       2
---------------------------------------------------------------------------
 3217- 3248 (35.61/12.89)	LLD..MYGAIapVEPLEME.RVFQELADNPSVAVQ....
 3255- 3289 (61.82/36.05)	LIN..CYGCM..LNDLDRAIATFDSIASHPSSQMRKDGA
 3291- 3326 (49.03/22.00)	LPNavSFEAL..LADEAGRIAD.DGLRGQPADPRLLDGA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.16|      15|      16|     982|     996|       3
---------------------------------------------------------------------------
  982-  996 (24.50/13.82)	LQSSLAASTAVTQPA
 1000- 1014 (23.65/12.98)	LGHSAAQDLAVSAHA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     121.87|      37|      40|    2290|    2328|       4
---------------------------------------------------------------------------
 2288- 2326 (58.11/43.70)	APLKVNTNTSAHDLVYRDLLyaSKRRDAQQVRLSVDAFN
 2327- 2363 (63.76/41.18)	ALPKDQKTTAGFNMVMESLL..SVRRSGQPVREITDTYN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.88|      14|      16|    2103|    2116|       5
---------------------------------------------------------------------------
 2103- 2116 (24.18/10.54)	RGAAQSAANAAHNS
 2121- 2134 (24.70/10.94)	RGAFQGASSGSTSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     166.74|      36|      37|    1015|    1050|       6
---------------------------------------------------------------------------
 1015- 1048 (57.77/27.18)	.....F.HPAM.SSFTPR.DASGATPFGDP..ASL.....PGF.TPSSLT
 1049- 1088 (40.45/16.50)	ESsptFgHPHY.K..TPRtPCSPVEEYRDG..ATI.....VDLhNGHRMG
 1089- 1121 (33.72/12.34)	ES.........aQSYRDR.NAASAPDLHAPdqHQL.....SGY.KADSF.
 1377- 1408 (34.79/13.01)	........PAG.SS......AAAEQTNEDP..ATLrslvkPPL.PFSRFT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     107.22|      36|      40|    2659|    2698|       7
---------------------------------------------------------------------------
 2661- 2698 (55.90/43.59)	DGTKIRNTVHTVI..QLSD....ILLAANRIVDAgsTLTYARLF
 2700- 2741 (51.32/26.93)	DKIDVTAAPHQQLgaQLSQltnrILTAADPANDA..KLNSIRLF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     111.85|      33|      40|     780|     813|       8
---------------------------------------------------------------------------
  780-  813 (51.21/33.40)	HSHADQSGSNwLVSSGSSTAPEGGQTAAAQSSDP
  823-  855 (60.64/34.31)	HPHLQSHGPT.LLQGQQETSPLGFTHPTSSKRKP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      67.31|      14|      15|    1905|    1918|       9
---------------------------------------------------------------------------
 1905- 1918 (23.25/14.65)	RARVRWRLAISSAV
 1923- 1936 (24.65/16.08)	RELVAWQRMIGSYV
 1938- 1950 (19.41/10.73)	STRAEERV.MGSVV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      44.34|      13|      15|     467|     479|      10
---------------------------------------------------------------------------
  467-  479 (24.16/16.71)	ANEHLTELCQS.FA
  484-  497 (20.18/12.32)	ASQHTEPNGQSpFA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     106.82|      33|      40|    1222|    1255|      11
---------------------------------------------------------------------------
 1222- 1255 (55.35/36.10)	EHPSSGNTGKGAERMDRQSFSETG....RLGtRYPATR
 1260- 1296 (51.47/28.80)	KMPSLRGEALLQLRRDRHGKSSPGlalnSLG.RSSSSR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     154.52|      40|      40|    2473|    2512|      12
---------------------------------------------------------------------------
 2449- 2471 (32.45/19.18)	.....K.PQETHQMQQ...SRKL.........AACKQVFDE
 2473- 2512 (68.24/51.00)	LLASQK.PQWKHDLNRIVWCSLLEAHFALNDPAGAIKLFEK
 2514- 2550 (53.83/38.19)	LQGGDNvPA....LDSSIISAIIRGFLDIHDTDTALHWFAK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      42.91|      11|      21|      15|      25|      13
---------------------------------------------------------------------------
   15-   25 (20.40/10.14)	ASIANSPSAHR
   37-   47 (22.51/12.17)	ASPSNNPSFPR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     163.97|      53|      60|     639|     698|      14
---------------------------------------------------------------------------
  637-  697 (85.17/60.33)	PyA.PgepdeasIARHRADRMPSTRADITPA......SMSFADFDFAMPIASSATPSHALPTAGQSVP
  698-  758 (78.80/42.78)	PgAsP.......LKREPASTEPVQAANSTEAfgqdlnWMHFLSPQISDAAVSSSEPAFALQIDSTSMP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.67|      20|      37|    2375|    2399|      15
---------------------------------------------------------------------------
 2375- 2399 (31.18/28.27)	RTYTALQLMsvahsSRNWFDDEKAY
 2414- 2433 (33.49/18.47)	RALSVLDLL.....ERSMFADTDAH
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.15|      21|      23|     304|     324|      16
---------------------------------------------------------------------------
  304-  324 (35.16/19.73)	SIDGKGKQSSLTSQ.QRQAHRR
  328-  349 (29.99/15.61)	SLKAKIIDSFAGAQpPSSKHKR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      31.21|      10|      17|    2068|    2081|      17
---------------------------------------------------------------------------
 2068- 2081 (12.97/20.03)	AAPTIPArtcrAKL
 2088- 2097 (18.24/ 9.78)	AMPVISA....AKL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.87|      16|      39|    2135|    2151|      18
---------------------------------------------------------------------------
 2135- 2151 (24.64/17.00)	TGSSASgWASGLSSGGS
 2175- 2190 (27.24/13.62)	TGRALS.QASTTSNSDS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.42|      23|      39|    2953|    2975|      20
---------------------------------------------------------------------------
 2953- 2975 (39.66/26.64)	GQELL..SFARPSGQNEAPRLYAKA
 2989- 3013 (33.76/21.32)	GLAFLigAFGRLGDVERVEEVYAMA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.51|      16|      17|    1417|    1432|      21
---------------------------------------------------------------------------
 1417- 1432 (29.09/16.80)	TATSISSRPTLRRW..ML
 1435- 1452 (25.41/13.64)	TAAWLIENPQFRSMygML
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.51|      14|      22|    1503|    1521|      22
---------------------------------------------------------------------------
 1503- 1521 (18.55/22.01)	EVAlpklrDLVRPSKHVAG
 1528- 1541 (21.96/11.31)	EVA.....EVLEPTRIAAG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      93.19|      35|     864|     592|     636|      23
---------------------------------------------------------------------------
  592-  636 (41.36/56.08)	GLGSNAMNDL.........KSMQSqPLtplkelvSFTlKVLNDANESAlAQSTA
 1453- 1496 (51.83/33.84)	GIGSMASSELaigdkievlETMAS.AL.......SIA.PVLTSTSEPA.ETSTA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.61|      24|     864|    1329|    1353|      24
---------------------------------------------------------------------------
 1329- 1353 (36.20/23.55)	DDSDDAlSDSEATALTLSPQ...DQATL
 2196- 2222 (37.41/20.01)	DDDDEA.RRQKAYKLRLDGQhhyDRSML
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     100.60|      30|      31|    2883|    2912|      26
---------------------------------------------------------------------------
 2883- 2912 (50.36/24.03)	QESAAVRGEVSSDAGSVSQFSASTPA.TTPP
 2914- 2944 (50.24/23.95)	QHSPLHRQDLPAPALSAFYTGTATSAfSFPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      36.03|      10|      21|    1824|    1833|      27
---------------------------------------------------------------------------
 1824- 1833 (18.89/ 9.25)	GGTSRNDGSA
 1844- 1853 (17.15/ 7.60)	GGLADGDQAA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.25|      20|      23|     536|     558|      29
---------------------------------------------------------------------------
  539-  558 (34.44/24.11)	GTSDQGMPL....AATTGVADERA
  561-  584 (29.80/11.64)	NARDEGLLQflwpAAWCLVVQEQA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.97|      17|      17|    1980|    1996|      31
---------------------------------------------------------------------------
 1980- 1996 (27.34/15.83)	AEKSSLVLLDAADFSQM
 2000- 2016 (32.63/20.59)	AEPMPMGWTQAVAESQM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.07|      13|      20|     362|     374|      32
---------------------------------------------------------------------------
  362-  374 (23.50/12.32)	PTSQSGSRS..TATP
  382-  396 (19.57/ 8.69)	PGLHKASFSgvTNSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      86.00|      28|      33|    2589|    2620|      33
---------------------------------------------------------------------------
 2589- 2620 (40.54/30.35)	QRVFHVYLENcverQVPAQISALIDLVSANVA
 2623- 2650 (45.46/24.16)	QRLLHAGSAD....QANASIDRALDAAAAFFA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      72.19|      22|      40|    1659|    1681|      34
---------------------------------------------------------------------------
 1659- 1681 (35.00/25.52)	KHVVVYTLQPPNSAACASTGFrG
 1702- 1723 (37.19/22.31)	EQLLVRAVSPSMMTESGSLGF.G
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      78.42|      24|      31|    2232|    2258|      37
---------------------------------------------------------------------------
 2232- 2258 (36.91/28.59)	SHMQvrfRHAFAAKQAPLLVTSSAQAD
 2264- 2287 (41.51/23.60)	SHNQ...RHASTLAATPTTTEASAGAE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     105.84|      32|     442|      50|      83|      38
---------------------------------------------------------------------------
   50-   83 (50.54/35.19)	ANAAFPGTVSAPRS.AAAPNsaLAPPKSIQHLSLL
  501-  533 (55.30/32.72)	AICAFSRPTSCPQSqQQEPH..LQDPQQLTDASLI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.03|      17|      35|    1759|    1783|      42
---------------------------------------------------------------------------
 1757- 1776 (23.52/27.33)	AGPISAAVQFPsfsLSTASA
 1782- 1798 (30.52/10.55)	AGQTNLSLSWP...LEPAAA
---------------------------------------------------------------------------




































Explaination for Stockholm format
  The  "Stockholm" format is a system for marking up features in a multiple alignment. These mark-up annotations are preceded by a 'magic' label, of which there are four types. The Stockholm format is used by HMMER, Pfam, and Belvu. Mark-up lines include any characters except whitespace. Underscore ("_") is used instead of space. 

 #=GR (seqname) PP (Generic per-Sequence AND per-Column markup, exactly 1 char per column) where PP is Posterior Probability  [0-9*], (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00) 
 
 #=GC PP_cons line is Stockholm-format consensus posterior probability annotation for the entire column.  It’s calculated simply as the arithmetic mean of the per-residue posterior probabilities in that column.  This should prove useful in phylogenetic inference applications, for example, where it’s common to mask away non confidently aligned columns of a multiple alignment. The PP_cons line provides an objective measure of the confidence assigned to each column.
 
 #=GC RF line is Stockholm-format reference coordinate annotation, with an x marking each column that the profile considered to be consensus.





Alignment of MDP03996 with Med13 domain of Kingdom Fungi
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