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Conserved domains on  [gi|1373971160|ref|XP_024363179|]
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rho-N domain-containing protein 1, chloroplastic-like isoform X1 [Physcomitrium patens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 429-478 1.73e-07

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 53.75  E-value: 1.73e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1373971160 429 VAQSEAVENGAVSKNLSSYKLPELRSMAKAKGLKGYSKLKKGELVELIAA 478
Cdd:PRK12678    8 ATATTDTAPRARGGGLAGMKLPELRALAKQLGIKGTSGMRKGELIAAIKE 57
PHA03325 super family cl25859
nuclear-egress-membrane-like protein; Provisional
 229-385 1.44e-03

nuclear-egress-membrane-like protein; Provisional


The actual alignment was detected with superfamily member PHA03325:

Pssm-ID: 223044  Cd Length: 418  Bit Score: 41.02  E-value: 1.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 229 LAALSQRHPSSFRKKSPI----PAARSRRTASKAEVDTAELVAAEDKETPMDSTVSSISARPERPAssfSRKSPIPKSRE 304
Cdd:PHA03325  251 LFQIGQLTSSAFMLNSSLptsaPKRRSRRAGAMRAAAGETADLADDDGSEHSDPEPLPASLPPPPV---RRPRVKHPEAG 327

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 305 RSSVSSSKRRSSAEVTSSAEAPSKPKFTKRSPISRNQNSSRATRSEKKSHSTE-----VAPTEVAPAQSEPVVSETESDS 379
Cdd:PHA03325  328 KEEPDGARNAEAKEPAQPATSTSSKGSSSAQNKDSGSTGPGSSLAAASSFLEDddfgsPPLDLTTSLRHMPSPSVTSAPE 407


                  ....*.
gi 1373971160 380 PVSPEL 385
Cdd:PHA03325  408 PPSIPL 413
PRK07003 super family cl35530
DNA polymerase III subunit gamma/tau;
131-292 3.55e-03

DNA polymerase III subunit gamma/tau;


The actual alignment was detected with superfamily member PRK07003:

Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 39.83  E-value: 3.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 131 STPSADAAAQPRIQHSESANVnVPAQTPKPEALPTIQQSESANVNVPAQTPTPEALPTIQQS-----KSANVNVPAQTQT 205
Cdd:PRK07003  375 RVAGAVPAPGARAAAAVGASA-VPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATadrgdDAADGDAPVPAKA 453

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 206 PEAIPTIQQSESANVNVPAQTPTLAALSQRHPSSFRKKSPIPAARSRRTASKAEVDTAELVAAEDKETPMDSTVSSISAR 285
Cdd:PRK07003  454 NARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEAR 533


                  ....*..
gi 1373971160 286 PERPASS 292
Cdd:PRK07003  534 PPTPAAA 540
 
Name Accession Description Interval E-value
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 429-478 1.73e-07

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 53.75  E-value: 1.73e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1373971160 429 VAQSEAVENGAVSKNLSSYKLPELRSMAKAKGLKGYSKLKKGELVELIAA 478
Cdd:PRK12678    8 ATATTDTAPRARGGGLAGMKLPELRALAKQLGIKGTSGMRKGELIAAIKE 57
Rho_N pfam07498
Rho termination factor, N-terminal domain; The Rho termination factor disengages newly ...
 444-476 3.80e-06

Rho termination factor, N-terminal domain; The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers. This domain is found to the N-terminus of the RNA binding domain (pfam07497).


Pssm-ID: 429493 [Multi-domain]  Cd Length: 43  Bit Score: 43.52  E-value: 3.80e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1373971160 444 LSSYKLPELRSMAKAKGLKGYSKLKKGELVELI 476
Cdd:pfam07498   2 LKEKTLSELREIAKELGIENYSRLRKQELIFAI 34
Rho_N smart00959
Rho termination factor, N-terminal domain; The Rho termination factor disengages newly ...
 443-476 6.73e-06

Rho termination factor, N-terminal domain; The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers. This domain is found to the N-terminus of the RNA binding domain.


Pssm-ID: 198027 [Multi-domain]  Cd Length: 43  Bit Score: 42.75  E-value: 6.73e-06
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1373971160  443 NLSSYKLPELRSMAKAKGLKGYSKLKKGELVELI 476
Cdd:smart00959   1 ELKKKTLSELLEIAKELGIENASRLRKQELIFAI 34
PHA03325 PHA03325
nuclear-egress-membrane-like protein; Provisional
 229-385 1.44e-03

nuclear-egress-membrane-like protein; Provisional


Pssm-ID: 223044  Cd Length: 418  Bit Score: 41.02  E-value: 1.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 229 LAALSQRHPSSFRKKSPI----PAARSRRTASKAEVDTAELVAAEDKETPMDSTVSSISARPERPAssfSRKSPIPKSRE 304
Cdd:PHA03325  251 LFQIGQLTSSAFMLNSSLptsaPKRRSRRAGAMRAAAGETADLADDDGSEHSDPEPLPASLPPPPV---RRPRVKHPEAG 327

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 305 RSSVSSSKRRSSAEVTSSAEAPSKPKFTKRSPISRNQNSSRATRSEKKSHSTE-----VAPTEVAPAQSEPVVSETESDS 379
Cdd:PHA03325  328 KEEPDGARNAEAKEPAQPATSTSSKGSSSAQNKDSGSTGPGSSLAAASSFLEDddfgsPPLDLTTSLRHMPSPSVTSAPE 407


                  ....*.
gi 1373971160 380 PVSPEL 385
Cdd:PHA03325  408 PPSIPL 413
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
131-292 3.55e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 39.83  E-value: 3.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 131 STPSADAAAQPRIQHSESANVnVPAQTPKPEALPTIQQSESANVNVPAQTPTPEALPTIQQS-----KSANVNVPAQTQT 205
Cdd:PRK07003  375 RVAGAVPAPGARAAAAVGASA-VPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATadrgdDAADGDAPVPAKA 453

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 206 PEAIPTIQQSESANVNVPAQTPTLAALSQRHPSSFRKKSPIPAARSRRTASKAEVDTAELVAAEDKETPMDSTVSSISAR 285
Cdd:PRK07003  454 NARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEAR 533


                  ....*..
gi 1373971160 286 PERPASS 292
Cdd:PRK07003  534 PPTPAAA 540
 
Name Accession Description Interval E-value
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 429-478 1.73e-07

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 53.75  E-value: 1.73e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1373971160 429 VAQSEAVENGAVSKNLSSYKLPELRSMAKAKGLKGYSKLKKGELVELIAA 478
Cdd:PRK12678    8 ATATTDTAPRARGGGLAGMKLPELRALAKQLGIKGTSGMRKGELIAAIKE 57
Rho_N pfam07498
Rho termination factor, N-terminal domain; The Rho termination factor disengages newly ...
 444-476 3.80e-06

Rho termination factor, N-terminal domain; The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers. This domain is found to the N-terminus of the RNA binding domain (pfam07497).


Pssm-ID: 429493 [Multi-domain]  Cd Length: 43  Bit Score: 43.52  E-value: 3.80e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1373971160 444 LSSYKLPELRSMAKAKGLKGYSKLKKGELVELI 476
Cdd:pfam07498   2 LKEKTLSELREIAKELGIENYSRLRKQELIFAI 34
Rho_N smart00959
Rho termination factor, N-terminal domain; The Rho termination factor disengages newly ...
 443-476 6.73e-06

Rho termination factor, N-terminal domain; The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers. This domain is found to the N-terminus of the RNA binding domain.


Pssm-ID: 198027 [Multi-domain]  Cd Length: 43  Bit Score: 42.75  E-value: 6.73e-06
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1373971160  443 NLSSYKLPELRSMAKAKGLKGYSKLKKGELVELI 476
Cdd:smart00959   1 ELKKKTLSELLEIAKELGIENASRLRKQELIFAI 34
PHA03325 PHA03325
nuclear-egress-membrane-like protein; Provisional
 229-385 1.44e-03

nuclear-egress-membrane-like protein; Provisional


Pssm-ID: 223044  Cd Length: 418  Bit Score: 41.02  E-value: 1.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 229 LAALSQRHPSSFRKKSPI----PAARSRRTASKAEVDTAELVAAEDKETPMDSTVSSISARPERPAssfSRKSPIPKSRE 304
Cdd:PHA03325  251 LFQIGQLTSSAFMLNSSLptsaPKRRSRRAGAMRAAAGETADLADDDGSEHSDPEPLPASLPPPPV---RRPRVKHPEAG 327

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 305 RSSVSSSKRRSSAEVTSSAEAPSKPKFTKRSPISRNQNSSRATRSEKKSHSTE-----VAPTEVAPAQSEPVVSETESDS 379
Cdd:PHA03325  328 KEEPDGARNAEAKEPAQPATSTSSKGSSSAQNKDSGSTGPGSSLAAASSFLEDddfgsPPLDLTTSLRHMPSPSVTSAPE 407


                  ....*.
gi 1373971160 380 PVSPEL 385
Cdd:PHA03325  408 PPSIPL 413
rho PRK09376
transcription termination factor Rho; Provisional
 442-476 2.03e-03

transcription termination factor Rho; Provisional


Pssm-ID: 236490 [Multi-domain]  Cd Length: 416  Bit Score: 40.51  E-value: 2.03e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1373971160 442 KNLSSYKLPELRSMAKAKGLKGYSKLKKGELVELI 476
Cdd:PRK09376    4 SELKNKSLSELLELAEELGIENASRLRKQELIFAI 38
PHA03247 PHA03247
large tegument protein UL36; Provisional
 136-384 2.80e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 40.69  E-value: 2.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160  136 DAAAQPRIQ-------HSESANVNVPAQTPKPEALPTIQQSESANVNVPAQTPTPE--------ALPTIQQSKSANVNVP 200
Cdd:PHA03247  2654 DDPAPGRVSrprrarrLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEpaphalvsATPLPPGPAAARQASP 2733

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160  201 AQTQTPEAIPTIQQSES-ANVNVPAQTPTLAALSQRHPSSFRKKSPIPAARSRRTASKAEV--------DTAELVAAEDK 271
Cdd:PHA03247  2734 ALPAAPAPPAVPAGPATpGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESreslpspwDPADPPAAVLA 2813

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160  272 ETPMDSTVSSISARPERPASSFSRKSPIPKSRERSSVSSSKRRSS----AEVTSSAEAPSKPKFTKRSPISR--NQNSSR 345
Cdd:PHA03247  2814 PAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPggdvRRRPPSRSPAAKPAAPARPPVRRlaRPAVSR 2893

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 1373971160  346 ATRSEKKSH-STEVAPTEVAPAQSEPVVSETESDSPVSPE 384
Cdd:PHA03247  2894 STESFALPPdQPERPPQPQAPPPPQPQPQPPPPPQPQPPP 2933
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
131-292 3.55e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 39.83  E-value: 3.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 131 STPSADAAAQPRIQHSESANVnVPAQTPKPEALPTIQQSESANVNVPAQTPTPEALPTIQQS-----KSANVNVPAQTQT 205
Cdd:PRK07003  375 RVAGAVPAPGARAAAAVGASA-VPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATadrgdDAADGDAPVPAKA 453

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 206 PEAIPTIQQSESANVNVPAQTPTLAALSQRHPSSFRKKSPIPAARSRRTASKAEVDTAELVAAEDKETPMDSTVSSISAR 285
Cdd:PRK07003  454 NARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEAR 533


                  ....*..
gi 1373971160 286 PERPASS 292
Cdd:PRK07003  534 PPTPAAA 540
PRK14949 PRK14949
DNA polymerase III subunits gamma and tau; Provisional
 142-389 3.67e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237863 [Multi-domain]  Cd Length: 944  Bit Score: 40.09  E-value: 3.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 142 RIQHSESANVNVPAQTPKP----EALPTIQQSESANVNVPAQTPTPEALPTIQQSKSANVNVPAQTQTPEAIPTIQQSES 217
Cdd:PRK14949  365 RWQVDDPAEISLPEGQTPSalaaAVQAPHANEPQFVNAAPAEKKTALTEQTTAQQQVQAANAEAVAEADASAEPADTVEQ 444

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 218 ANVNVPAQTPTLAA-----LSQRHPSSFRKKSPIPAARSRRTASKAEVDTAELVAAEDKETPMDSTVSSISARPERPASS 292
Cdd:PRK14949  445 ALDDESELLAALNAeqaviLSQAQSQGFEASSSLDADNSAVPEQIDSTAEQSVVNPSVTDTQVDDTSASNNSAADNTVDD 524

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 293 fsrkSPIPKSRERSSVSSSKRRSSAEVTSSAEAPSKPKFTKRSPISRNQNSSRATRSEKKSHSTEVAPTEVAPAQSEPVV 372
Cdd:PRK14949  525 ----NYSAEDTLESNGLDEGDYAQDSAPLDAYQDDYVAFSSESYNALSDDEQHSANVQSAQSAAEAQPSSQSLSPISAVT 600

                         250
                  ....*....|....*..
gi 1373971160 373 SETesdspVSPELKEIL 389
Cdd:PRK14949  601 TAA-----ASLADDDIL 612
PRK14948 PRK14948
DNA polymerase III subunit gamma/tau;
131-324 6.19e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237862 [Multi-domain]  Cd Length: 620  Bit Score: 39.18  E-value: 6.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 131 STPSADAAAQPRIQHSESANVNVPAQTPKPEALPTIQQSESANVNVPAQTPTPEALPTIQQSKSANVNVPAQTQTPEAI- 209
Cdd:PRK14948  366 SEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAEPTEPSPTPPANAANAPPSLNLEELw 445

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 210 ---------PTIQ------------QSESANVNVPAQ--------TPTLAA-------------LSQRHPSSFRKKSPIP 247
Cdd:PRK14948  446 qqilaklelPSTRmllsqqaelvslDSNRAVIAVSPNwlgmvqsrKPLLEQafakvlgrsiklnLESQSGSASNTAKTPP 525

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1373971160 248 AARSRRTASKAEVDTAELVAAEDKETPMDSTVSSISARPERPASSFSRKSPIPKSRERSSVSSSKRRSSAEVTSSAE 324
Cdd:PRK14948  526 PPQKSPPPPAPTPPLPQPTATAPPPTPPPPPPTATQASSNAPAQIPADSSPPPPIPEEPTPSPTKDSSPEEIDKAAK 602
PRK07994 PRK07994
DNA polymerase III subunits gamma and tau; Validated
 124-274 8.91e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236138 [Multi-domain]  Cd Length: 647  Bit Score: 38.69  E-value: 8.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 124 LFFSFSKSTPSADAAAQPRIQHSESANVNVPAQTPKPealPTIQQSESANVNVPAQTPTPEALPTIQQSKSANVNVPAQT 203
Cdd:PRK07994  357 LAFHPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAP---PQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQRAQ 433

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1373971160 204 QTPEAIPTIQQSESANVNVPAQTPTLAALSQRHPSSfrKKSPIPAARSRRTASKAEVDTAELVAAEDKETP 274
Cdd:PRK07994  434 GATKAKKSEPAAASRARPVNSALERLASVRPAPSAL--EKAPAKKEAYRWKATNPVEVKKEPVATPKALKK 502
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 159-298 9.95e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 38.54  E-value: 9.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 159 KPEALPTIQQSESANVNVPAQTPTPEALPtiqqsksanVNVPAQTQTPEAIPTIQQSESANVNVPAQTPTLAALSQRHPS 238
Cdd:PRK14951  365 KPAAAAEAAAPAEKKTPARPEAAAPAAAP---------VAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPA 435

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373971160 239 SFRKKSPIPAARSrrtASKAEVDTAELVAAEDKETPMDSTVSSISARPERPASSFSRKSP 298
Cdd:PRK14951  436 AAPAAAPAAVALA---PAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPTE 492
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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