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PANDIT
Protein and Associated NucleotideDomains with Inferred Trees
(View summary and phylogenies for PF03874 - RNA_pol_Rpb4)
FAM  PF03874
PID  RNA_pol_Rpb4
DES  RNA polymerase Rpb4
IPR  IPR005574
ANO  15
ALN  180
AID  0.257434
APH  ((((O27379_METTH/10-116:0.43154,(Y039_METJA/15-115:0.48586,O58854_PYRHO/7-121:0.49487):0.15792):0.11596,(Q9HQG9_HALN1/8-119:0.77243,O28742_ARCFU/9-119:0.46899):0.09816):0.34928,((((((Q9VEA5_DROME/35-148:0.21610,RPB4_HUMAN/27-140:0.03552):0.24698,O02092_CAEEL/118-231:0.27169):0.20176,O48890_ARATH/19-137:0.64565):0.18524,O96150_PLAF7/19-130:1.01982):0.04777,(RPB4_SCHPO/20-133:0.53098,RPB4_YEAST/45-220:0.63690):0.15638):0.98280,Q9YEM9_AERPE/9-116:1.42005):0.27940):0.91019,Q9HIN7_THEAC/3-105:0.06361,Q97BZ0_THEVO/1-103:0.33440);
ATP  ((((O27379_METTH/10-116,(Y039_METJA/15-115,O58854_PYRHO/7-121)),(Q9HQG9_HALN1/8-119,O28742_ARCFU/9-119)),((((((Q9VEA5_DROME/35-148,RPB4_HUMAN/27-140),O02092_CAEEL/118-231),O48890_ARATH/19-137),O96150_PLAF7/19-130),(RPB4_SCHPO/20-133,RPB4_YEAST/45-220)),Q9YEM9_AERPE/9-116)),Q9HIN7_THEAC/3-105,Q97BZ0_THEVO/1-103);
ATL  11.5388
DNO  15
DLN  540
DID  0.403587
DPH  ((O28742_ARCFU/9-119:0.32248,(((Y039_METJA/15-115:0.41011,O58854_PYRHO/7-121:0.32286):0.10580,((Q97BZ0_THEVO/1-103:0.18403,Q9HIN7_THEAC/3-105:0.23449):0.21522,(O96150_PLAF7/19-130:0.51659,((RPB4_YEAST/45-220:0.48826,RPB4_SCHPO/20-133:0.42288):0.09444,(O48890_ARATH/19-137:0.45894,(O02092_CAEEL/118-231:0.25791,(RPB4_HUMAN/27-140:0.16062,Q9VEA5_DROME/35-148:0.25496):0.23811):0.17227):0.11969):0.17565):0.37128):0.32611):0.14328,O27379_METTH/10-116:0.42466):0.11048):0.19962,Q9HQG9_HALN1/8-119:0.35055,Q9YEM9_AERPE/9-116:0.78264);
DTP  ((O28742_ARCFU/9-119,(((Y039_METJA/15-115,O58854_PYRHO/7-121),((Q97BZ0_THEVO/1-103,Q9HIN7_THEAC/3-105),(O96150_PLAF7/19-130,((RPB4_YEAST/45-220,RPB4_SCHPO/20-133),(O48890_ARATH/19-137,(O02092_CAEEL/118-231,(RPB4_HUMAN/27-140,Q9VEA5_DROME/35-148))))))),O27379_METTH/10-116)),Q9HQG9_HALN1/8-119,Q9YEM9_AERPE/9-116);
DTL  7.86393
RID  0.257434
RPH  ((((O27379_METTH/10-116:0.43154,(Y039_METJA/15-115:0.48586,O58854_PYRHO/7-121:0.49487):0.15792):0.11596,(Q9HQG9_HALN1/8-119:0.77243,O28742_ARCFU/9-119:0.46899):0.09816):0.34928,((((((Q9VEA5_DROME/35-148:0.21610,RPB4_HUMAN/27-140:0.03552):0.24698,O02092_CAEEL/118-231:0.27169):0.20176,O48890_ARATH/19-137:0.64565):0.18524,O96150_PLAF7/19-130:1.01982):0.04777,(RPB4_SCHPO/20-133:0.53098,RPB4_YEAST/45-220:0.63690):0.15638):0.98280,Q9YEM9_AERPE/9-116:1.42005):0.27940):0.91019,Q9HIN7_THEAC/3-105:0.06361,Q97BZ0_THEVO/1-103:0.33440);
RTP  ((((O27379_METTH/10-116,(Y039_METJA/15-115,O58854_PYRHO/7-121)),(Q9HQG9_HALN1/8-119,O28742_ARCFU/9-119)),((((((Q9VEA5_DROME/35-148,RPB4_HUMAN/27-140),O02092_CAEEL/118-231),O48890_ARATH/19-137),O96150_PLAF7/19-130),(RPB4_SCHPO/20-133,RPB4_YEAST/45-220)),Q9YEM9_AERPE/9-116)),Q9HIN7_THEAC/3-105,Q97BZ0_THEVO/1-103);
RTL  11.5388
LNK  O02092_CAEEL/118-231:O02092:AF000264
LNK  O27379_METTH/10-116:O27379:AE000896
LNK  O28742_ARCFU/9-119:O28742:AE000997
LNK  O48890_ARATH/19-137:O48890:AF016511
LNK  O58854_PYRHO/7-121:O58854:BA000001
LNK  O96150_PLAF7/19-130:O96150:AE001382
LNK  Q97BZ0_THEVO/1-103:Q97BZ0:BA000011
LNK  Q9HIN7_THEAC/3-105:Q9HIN7:AL445067
LNK  Q9HQG9_HALN1/8-119:Q9HQG9:AE005045
LNK  Q9VEA5_DROME/35-148:Q9VEA5:AE003721
LNK  Q9YEM9_AERPE/9-116:Q9YEM9:BA000002
LNK  RPB4_HUMAN/27-140:O15514:U89387
LNK  RPB4_SCHPO/20-133:O74825:AB019575
LNK  RPB4_YEAST/45-220:P20433:M27253
LNK  Y039_METJA/15-115:Q60351:U67462
AMK  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx
DMK  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................................................................................................................................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
NAM  Q9YEM9_AERPE/9-116
ASQ  LEYKAVPYQVAKKYMYE---------RVREGDI............................................................ISIQESTWEYFRKVVFWDDPEAASELVEEIVKEG-VSREAAANIASICPKTEGELRSILEMDRSI.-TSVHEMASKLYPIVSKYCKD
DSQ  CTAGAGTATAAGGCGGTGCCCTACCAGGTAGCCAAGAAGTATATGTACGAG---------------------------AGGGTTAGGGAGGGCGACATA....................................................................................................................................................................................ATATCGATACAGGAGTCGACTTGGGAGTACTTCAGGAAGGTAGTGTTCTGGGACGACCCGGAGGCTGCCTCCGAGCTTGTTGAGGAGATTGTGAAGGAGGGT---GTCAGCCGTGAGGCCGCGGCGAACATCGCGAGCATATGCCCCAAGACCGAGGGCGAGCTCAGGAGCATTCTCGAGATGGACAGGAGCATA...---ACCTCCGTACACGAGATGGCTAGCAAACTGTACCCCATAGTTTCCAAATACTGCAAGGAC
TRN  10010101100011011
NAM  O27379_METTH/10-116
ASQ  LESEPVSMAEVKEILEK---------FGEDHEL............................................................TYEQNLVLDHVTRFSRLDPEKSRELVEELMDIPN-IKRRHAVKIADIMPVDISDLRLIFAKERVP.-IKADDL-PGILEVIDKYRVE
DSQ  CTGGAAAGTGAACCTGTTTCTATGGCAGAGGTTAAGGAAATCCTTGAAAAA---------------------------TTTGGGGAAGACCATGAACTC....................................................................................................................................................................................ACATACGAGCAGAACCTTGTCCTTGACCATGTAACCCGTTTTTCAAGGCTTGACCCTGAAAAGAGCAGGGAGCTGGTGGAGGAACTGATGGACATCCCCAAC---ATCAAAAGGAGGCATGCTGTTAAAATTGCAGATATAATGCCGGTGGACATATCCGACCTCCGTTTAATCTTTGCCAAGGAGAGGGTTCCC...---ATAAAGGCTGATGACCTT---CCAGGCATACTCGAGGTAATAGATAAATACCGGGTCGAA
TRN  10010101100011000
NAM  O28742_ARCFU/9-119
ASQ  RDFEYITISEAKEIMEEIAKK-----RQEEAEL............................................................LFETRRALKHLRLFAKLPADKAKELVDELVKLPQVGSKEIAVKLADIMPRIPDEVRIIYAKERVT.-LTPEQI-QEILDVIDKYRI-
DSQ  AGGGATTTTGAATACATCACAATTTCTGAAGCGAAAGAAATAATGGAAGAAATAGCCAAAAAA---------------AGGCAGGAGGAGGCCGAGCTT....................................................................................................................................................................................TTGTTTGAAACCAGGAGGGCTTTAAAGCACCTCCGCCTTTTCGCCAAACTTCCGGCAGATAAGGCAAAGGAGCTTGTTGATGAGCTTGTCAAACTGCCCCAGGTGGGCAGCAAGGAGATAGCCGTAAAGCTTGCGGATATAATGCCGCGAATACCTGACGAAGTGAGGATTATTTACGCTAAGGAAAGAGTTACT...---CTGACACCCGAGCAAATT---CAGGAAATTCTGGACGTCATCGACAAGTATCGTATT---
TRN  10010101100011010
NAM  O58854_PYRHO/7-121
ASQ  LGERYITISEAKEILLKKYEEGIK--AGIEEPL............................................................FYEARLALEHAEKFAKLPAEKARKAIEELMSEFEWMNERIAAKLVDIMPEDNLDLRVIFAKEEHQ.-PTPEEM-KKILEILDKYREE
DSQ  CTTGGCGAGAGGTACATAACGATATCCGAAGCAAAAGAGATATTACTTAAGAAATATGAAGAAGGAATAAAA------GCTGGGATAGAAGAGCCATTG....................................................................................................................................................................................TTCTATGAAGCAAGGCTAGCTCTAGAGCATGCTGAAAAGTTCGCTAAGTTGCCAGCTGAAAAAGCTAGAAAAGCTATTGAAGAGCTAATGTCAGAATTTGAATGGATGAACGAGAGGATAGCCGCAAAATTAGTTGATATAATGCCAGAGGATAACCTCGATTTAAGGGTTATATTTGCAAAGGAGGAGCATCAG...---CCAACACCAGAGGAAATG---AAGAAGATACTTGAAATCCTTGATAAGTATAGAGAAGAG
TRN  10010101110011000
NAM  Y039_METJA/15-115
ASQ  LGERYVTVSEAAEIMYN---------RAQIGEL............................................................SYEQGCALDYLQKFAKLDKEEAKKLVEELISLG--IDEKTAVKIADILPEDLDDLRAIYYKRELP.----ENA-EEILEIVRKYI--
DSQ  CTTGGAGAGAGGTATGTAACAGTATCAGAGGCTGCTGAAATTATGTATAAT---------------------------AGAGCCCAAATTGGAGAGTTA....................................................................................................................................................................................TCTTACGAACAGGGATGTGCTTTAGATTATTTACAAAAGTTTGCCAAATTAGATAAAGAAGAGGCAAAAAAATTGGTTGAAGAGTTAATATCTTTAGGA------ATAGATGAAAAAACAGCAGTTAAAATAGCTGATATATTACCTGAAGATTTAGATGATTTGAGAGCAATATATTACAAAAGAGAATTGCCA...------------GAAAATGCT---GAGGAAATCTTAGAAATCGTTAGGAAATATATT------
TRN  10010101110011000
NAM  Q9HQG9_HALN1/8-119
ASQ  VETEPLTVSEAKALLSEVETERA---LDEDREL............................................................RFELSRAIEHANRFALLEPAESREFVDELLALDVLDDEAVAYKIVDLLPRTRTELRSVFANERYA.-MSGDEL-DEILDVVAKYV--
DSQ  GTCGAGACGGAGCCGCTCACGGTCTCGGAAGCGAAAGCGCTGCTCTCCGAGGTCGAGACCGAGCGCGCC---------CTCGACGAGGACCGTGAGCTT....................................................................................................................................................................................CGCTTCGAGCTGTCCCGCGCCATCGAGCACGCCAATCGGTTCGCGTTGCTGGAGCCGGCGGAGTCCCGGGAGTTCGTCGACGAACTGCTCGCGCTCGACGTGCTTGACGACGAGGCCGTGGCGTACAAGATCGTGGACCTGCTTCCACGCACGCGAACGGAGTTGCGGTCGGTGTTCGCCAACGAACGCTACGCG...---ATGTCCGGCGACGAGCTG---GACGAGATTCTCGACGTCGTCGCGAAGTACGTC------
TRN  11011101101011011
NAM  Q97BZ0_THEVO/1-103
ASQ  MEKKYISIPEVYNILSK------------KEQL............................................................TDMEKENLEYAGKFSRVDPSVIDRVKGDISGIAK-LPEKVIVKILDLKPGTPADITSILSTYNVM.-ISDEDL-NALADYLKKLKF-
DSQ  ATGGAGAAAAAGTATATCAGCATACCCGAAGTTTACAATATACTGTCGAAA------------------------------------AAAGAACAGCTG....................................................................................................................................................................................ACCGACATGGAAAAAGAAAACTTAGAGTATGCTGGCAAATTCTCAAGAGTAGATCCTTCTGTAATAGATAGGGTAAAGGGGGATATTTCTGGAATAGCTAAG---CTGCCAGAAAAAGTTATTGTGAAAATTCTTGATCTTAAACCGGGGACCCCGGCAGATATAACATCTATACTTTCAACTTACAACGTTATG...---ATTTCTGACGAAGATTTA---AATGCTCTTGCCGACTATCTCAAAAAATTAAAATTC---
TRN  10010101100011000
NAM  Q9HIN7_THEAC/3-105
ASQ  MEKKYISIPEVIDLLSN------------RENL............................................................TDLEKENLAYAEKFARIDPKAIKKVREDILSIVD-MPEKALVKILDLKPETPGELTAILSTYGVM.-ISDENL-NALTDYLKKLRF-
DSQ  ATGGAGAAGAAATACATAAGCATACCAGAGGTTATCGATCTTCTTTCCAAT------------------------------------CGAGAAAATCTT....................................................................................................................................................................................ACCGATCTTGAAAAGGAAAATCTCGCATATGCTGAGAAATTTGCAAGGATAGATCCAAAAGCGATAAAGAAGGTGAGGGAGGACATTCTATCCATAGTGGAT---ATGCCTGAAAAGGCGCTTGTTAAAATACTGGATCTTAAGCCAGAAACTCCCGGGGAACTCACAGCAATTCTATCAACGTACGGAGTCATG...---ATATCCGACGAAAATTTA---AATGCACTTACCGACTACCTTAAGAAGCTAAGGTTC---
TRN  10010101100011000
NAM  O96150_PLAF7/19-130
ASQ  KNCKCLNLCELQLILGDQLRLTSK--RNEEAQA............................................................--LIKSSYDYANKFAAIKNRSSIVDIRTNLERIGDLHEYEIAMLVNLLPKTILEARYLIPSLIR-.-LNDETL-NSILEHLISYKMY
DSQ  AAGAATTGTAAATGTTTGAATTTATGTGAGCTTCAATTAATTTTGGGAGACCAGCTTCGATTAACATCCAAG------AGAAATGAAGAAGCTCAAGCA....................................................................................................................................................................................------TTGATTAAATCGTCCTATGATTATGCCAATAAATTTGCTGCAATAAAAAATAGAAGTTCAATTGTCGATATTAGAACTAACTTAGAACGTATAGGCGATTTACATGAATATGAAATAGCCATGTTAGTTAATCTTTTACCTAAGACCATATTAGAAGCTAGATATTTAATTCCTTCGTTAATTCGT---...---TTAAATGACGAAACCTTA---AATTCTATTTTAGAACATCTTATAAGCTATAAAATGTAC
TRN  10010101110011000
NAM  RPB4_YEAST/45-220
ASQ  EELIALNLSEARLVIKEALVERRRAFKRSQKKHkkkhlkhenandettavededddldeddvnaddddfmhsetrekelesidvlleqttggnNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTG-LHPFEVAQLGSLACDTADEAKTLIPSLNNK.-ISDDEL-ERILKELSNLETL
DSQ  GAGGAATTGATTGCCTTGAACCTAAGTGAAGCCAGGTTAGTAATCAAAGAAGCTCTTGTAGAACGTAGGAGAGCATTTAAAAGATCGCAAAAAAAACACaagaagaagcatttgaagcacgaaaacgccaatgatgaaactacggcagtagaggatgaagatgatgatctggatgaagatgacgtcaacgctgatgatgatgattttatgcattctgaaactagggagaaggagttggagtctatcgacgttctgttagaacagacaacgggaggaaatAATAAAGATTTGAAAAATACCATGCAGTATTTAACAAATTTCTCCCGATTTAGAGACCAAGAAACCGTCGGGGCAGTTATACAGCTTCTGAAAAGCACTGGG---TTACATCCTTTTGAAGTGGCGCAACTAGGTTCTTTGGCCTGTGACACAGCTGATGAAGCAAAGACTTTAATTCCAAGCTTAAACAATAAA...---ATATCAGACGATGAGTTG---GAAAGGATACTAAAGGAATTGTCAAACCTAGAAACACTC
TRN  10010101100011000
NAM  RPB4_SCHPO/20-133
ASQ  ENEDMLTVSEAKILIETVLAQRARE-TNGEIPM............................................................TDVMKKTVAYFNVFARFKTAEATYACERILGNR--FHKFERAQLGTLCCEDAEEARTLIPSLANK.-IDDQNL-QGILDELSTLRKF
DSQ  GAGAATGAGGATATGTTGACGGTTTCAGAGGCCAAAATCCTTATTGAAACAGTTCTGGCACAACGAGCACGCGAA---ACTAATGGTGAGATTCCAATG....................................................................................................................................................................................ACTGATGTGATGAAAAAAACAGTAGCTTACTTCAATGTTTTTGCTCGGTTTAAAACGGCTGAAGCCACTTATGCATGTGAAAGAATTCTTGGTAATCGA------TTCCATAAATTTGAACGTGCACAATTGGGAACACTCTGCTGCGAAGACGCTGAAGAGGCTAGGACCTTGATTCCTAGTCTCGCGAATAAA...---ATTGATGACCAAAATCTT---CAAGGCATCTTGGATGAGCTTTCCACTTTGCGTAAATTT
TRN  10010101100011001
NAM  O48890_ARATH/19-137
ASQ  LKAKCLMNCEVSLILEHKFEQLQQISEDPMNQV............................................................SQVFEKSLQYVKRFSRYKNPDAVRQVREILSRHQ-LTEFELCVLGNLCPETVEEAVAMVPSLKTKgRAHDDEAIEKMLNDLSLVKRF
DSQ  TTGAAGGCAAAGTGCTTAATGAACTGTGAAGTCTCTTTGATTCTTGAGCACAAGTTTGAACAGCTTCAGCAAATCTCAGAGGATCCTATGAATCAAGTT....................................................................................................................................................................................TCTCAAGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAAATACTAAGCAGACATCAA---CTCACTGAGTTTGAGCTATGTGTTCTTGGCAATCTCTGTCCTGAAACTGTTGAAGAAGCAGTGGCAATGGTTCCTTCTCTTAAGACAAAAggaAGAGCTCATGATGATGAAGCTATTGAGAAGATGCTCAATGATCTCTCACTTGTCAAGAGATTC
TRN  10010101110011000
NAM  O02092_CAEEL/118-231
ASQ  TTCDALLTAEVYLLLEHRRQSSES--KDEIEEM............................................................SEVFIKTLNYARRMSRFKNRETIRAVRAIFSEKH-LHKFEVAQIANLCPENAEEAKALVPSLENK.-IEESEL-EEVLKDLQSKRTF
DSQ  ACAACATGCGACGCTCTTCTGACCGCTGAGGTTTACTTGCTTCTGGAGCATCGTCGTCAATCGAGTGAAAGC------AAAGACGAAATTGAAGAGATG....................................................................................................................................................................................AGCGAGGTCTTCATCAAAACTCTCAACTACGCTCGCCGCATGTCTCGATTCAAAAATCGCGAAACTATCCGTGCAGTTCGAGCGATTTTCTCCGAGAAGCAT---CTTCACAAATTCGAAGTTGCGCAGATTGCCAATCTCTGCCCTGAAAATGCCGAAGAAGCCAAAGCACTAGTTCCTTCTTTGGAAAACAAA...---ATCGAGGAGTCTGAACTA---GAGGAAGTTCTCAAGGATCTGCAATCCAAAAGAACATTC
TRN  10010101100011011
NAM  RPB4_HUMAN/27-140
ASQ  ETAETLLNSEVHMLLEHRKQQNES--AEDEQEL............................................................SEVFMKTLNYTARFSRFKNRETIASVRSLLLQKK-LHKFELACLANLCPETAEESKALIPSLEGR.-FEDEEL-QQILDDIQTKRSF
DSQ  GAAACAGCTGAGACACTTCTAAATTCAGAAGTTCATATGCTTCTGGAACATCGAAAGCAGCAGAATGAGAGT------GCAGAGGACGAACAGGAGCTC....................................................................................................................................................................................TCAGAAGTCTTCATGAAAACATTAAACTACACAGCCCGTTTCAGTCGTTTCAAAAACAGAGAGACCATTGCCAGTGTTCGTAGCTTGCTACTCCAGAAAAAG---CTTCATAAGTTTGAGTTGGCCTGTTTGGCCAACCTTTGCCCAGAGACTGCTGAGGAGTCCAAGGCTCTAATCCCAAGCTTGGAGGGACGG...---TTTGAAGATGAGGAGCTG---CAGCAGATTCTTGATGATATCCAGACAAAGCGCAGCTTT
TRN  10010101100011000
NAM  Q9VEA5_DROME/35-148
ASQ  ENAETLLISEVHMLLDHRKRQNES--ADEEQEF............................................................SEVFMKTYAYTDSFRKFKNKETIMSARSLLMQKK-LHKFELAALGNLCPEAPEEAKALIPSLEGR.-FEDEEL-RQILDDIGTKRSL
DSQ  GAAAATGCCGAGACGCTGCTGATATCGGAGGTGCACATGCTTCTCGATCACCGAAAGCGACAAAACGAATCC------GCCGACGAGGAGCAAGAGTTC....................................................................................................................................................................................TCCGAGGTCTTCATGAAGACGTACGCCTACACGGATAGTTTTCGAAAGTTCAAAAACAAGGAGACCATAATGTCTGCGCGAAGCTTGCTGATGCAGAAAAAG---CTGCACAAATTCGAACTGGCGGCACTGGGTAATTTGTGTCCGGAGGCGCCCGAGGAGGCCAAGGCGCTGATTCCTTCACTAGAGGGTCGC...---TTCGAGGATGAGGAGCTG---CGCCAAATACTCGACGATATCGGCACTAAACGCAGCTTA
TRN  10010101100011000
//