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Entrez CDD Structure Protein Help
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CHL00018: rpoC1, with user query added  
RNA polymerase beta' subunit
Statistics
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PSSM-Id: 100139
View PSSM: CHL00018
Aligned: 100 rows
Created: 22-Jul-2008
Updated: 31-Jul-2008
Structure
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Aligned Rows:
CHL00018 is classified as a model that may span more than one domain.
CHL00018 is not assigned to any domain superfamily.
Sequence Alignment?
Format: Row Display: Color Bits: Type Selection:

gi 29565714     1 .[275].EPKWMVLCLLPVLPPEPRPIVQL.[1].EGGLITSSDLNELYRRVINRNNTLT.[3].ARSGSESFVICQK 340
query           1 .[235].RPDWMIVTVLPVPPLAVRPAVVM     FGAAKNQDDLTHKLSDIIKANNELR.[1].NEASGAAAHVIQE 297
gi 30352025     1 .[263].KPEWMVLYFIPVLPPELRPIVEL     YEGELITSDLNELYRKIIYRNNTLR.[5].SEFTPEGLIVCQK 329
gi 139390339    1 .[259].EPEWMVLCLLPVLPPELRPIIQI     EGGKLMSSDINELYRRVIYRNNTLT.[5].SRSTPGELVMCQE 325
gi 124112109    3 .[250].KPEWMILSILPVLPPDLRPMVQL     DGGQFATSDLNDLYRRVINRNNRLS.[3].TMLAPEIVVRSEK 316
gi 159161244    8 .[259].EPKWMVLCLLPVLPPELRPIIQI     DGGKLMSSDINELYRRVIYRNNTLT.[5].SRSTPGELVMCQE 332
gi 11467372     2 .[242].KPEWMILSLIPVIPPDLRPMVQL     DGGRFATSDLNDLYRRVINRNNRLL.[3].EVFAPEIVVRNEK 307
gi 150251450    1 .[259].EPEWMVLCPLPVLPPELRPIVQL     GGGELITSDPNELYRRVIYRNNTLT.[5].SRSTPGGLVICQK 325
gi 34501435     1 .[256].KPEWMVLSLLPVLPPELRPMIEL     GEGELITSDLNELYRRVIYRNNTLI.[5].SGSTPGGLVVCQI 322
gi 134093188    8 .[259].EPEWMVLCLLPVLPPELRPIIQI     DGGKLMSSDINELYRRVIYRNNTLT.[5].SRSTPGELVMCQE 332

gi 29565714   341      KLIQEAVDALLDNGICGQP     MRDS.[1].DRP     YKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVV 401
query         298 .[2].KMLQFHVATLVDNDMPGMP.[2].MQKS     GKP     LKAIKARLKGKEGRIRGNLMGKRVDFSARTVITP 361
gi 30352025   330      RLVQEAVDALIGSGIRGQP     MRDI.[1].NRP     YKSFSEVIEGKEGRFRENLLGKRVDYSGRSVIVV 390
gi 139390339  326      KLVQEAVDTLLDNGIRGQP     MRDG.[1].NKV     YKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVV 386
gi 124112109  317      RMLQEAVDALIDNGKRGRQ     ALVG.[1].NKI.[1].LKSLSDIIKGKQGRFRQNLLGKRVDYSGRSVIVV 378
gi 159161244  333      KLVQEAVDTLLDNGIRGQP     MRDG.[1].NKV     YKSFSDIIEGKEGRFRETLLGKRVDYSGRSVIVV 393
gi 11467372   308      RILQEAVDALIDNGRRGRI     VVGA.[1].NRP     LKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVV 368
gi 150251450  326      KLVQEAVDALLDNGIRGQP     MRDS.[1].DRP     YKSFSDVIEGKEGRSRENLLGKRVDYSGRSVIVV 386
gi 34501435   323      RLVQEAVDGLIDNGIRGQP     MKDS.[1].NRP     YKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVV 383
gi 134093188  333      KLVQEAVDTLLDNGIRGQP     MRDG.[1].NKV     YKSFSDVIEGKEGRFRETMLGKRVDYSGRSVIVV 393

gi 29565714   402 GPFLSLYQCGLPSEIAI     ELFQAFVI     RSLIGRHIAPNLR.[1].AKSMIRDKGPIV      WEVLQEVMQ 461
query         362 DPNLRIDQVGVPRSIAQ.[5].ELVTPFNI.[3].QELVRRGNSQYPG     AKYIVRDNGERI.[16].YKVERHLRD 444
gi 30352025   391 GPSLSLHQCGLPREMAI     ELFQAFVI     RNLIGXHLACNLR.[1].AKCMIRKGNPII      WEVLREVMR 450
gi 139390339  387 GPSLSLHRCGLPREIAI     ELFQTFVI     RGLIRQHLASNIG.[1].AKSQIRENKPIV      WEILQEVMQ 446
gi 124112109  379 GPQLKLHQCGLPKEMAI     ELFQPFVI     HNLINQGLANNIK.[1].AKRKLQNNDPSI      WEVLKQVIQ 438
gi 159161244  394 GPSLSLHQCGLPREIAI     ELFQPFVI     RDLIKQHLASNIG.[1].AKSKIREKEPII      WEILQDVMQ 453
gi 11467372   369 GLQLKLYQCGLPWEMAI     ELFQPFVI     HRLIHQGLVNNIK.[1].AKKLIQSNDPII      RDILEEVIQ 428
gi 150251450  387 GPSLPLHQCGLPREIAI     ELFQAFVI     RGLIRRHFAPNLR.[1].AKSIIRDKEPIV      WEVLQGVMQ 446
gi 34501435   384 GPFLSLHQCGLPREMAI     ELFQAFVI     RGLIGRHLAPNLR.[1].AKSMIQNKEPII      WKILQEIMQ 443
gi 134093188  394 GPSLSLHRCGLPREIAI     ELFQTFVI     RGLIRQHLASNIG.[1].AKSKIREKEPIV      WGILQEVMR 453

gi 29565714   462 GHPVLLNRAPTLHKLGIQAFQPILVEGRAIRLHPSVCGGFNADFDGDQMAVHVPLSLEARAEARLLMFSETNLLSPAIGD 541
query         445 DDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANK 524
gi 30352025   451 GHPVLLNRAPTLHRLGIQAFQPLLIEGRAIRLHPLVRGGSNADLDGDQMAVHVPLSVEAQIEARLLMFSHLNLLSPATGD 530
gi 139390339  447 GHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGD 526
gi 124112109  439 GHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHIPLSLEAQTEARLLMLASSNLLSPATGQ 518
gi 159161244  454 GHPVLLNRAPTLHRLGIQAFQPVLVEGRVICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGD 533
gi 11467372   429 NHPVLLNRAPTLHRLSIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEARLLMLASNNLLSPATGQ 508
gi 150251450  447 GHPVSLNRAPTLHRLGIQAFQPILVEGRAIRLHPLVCGGFNADSDGDQMAVHVPLSLEAQAEARLLMFSHTNLLSPAIGD 526
gi 34501435   444 GHPVLLNRAPTLHRLGIQAFQPILIKGRAIRLHPLVCGGFNADFDGDQMAVHIPLSLEAQAEARLLMFSHTNLLSPATGD 523
gi 134093188  454 GHPILLNRAPTLHRLGIQAFQPILVEGRAICLHPLVRKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGD 533

gi 29565714   542 PISIPTQDMLLGLYIST.[3].S.[126]. 688
query         525 PVMGIVQDTLTAVRKMT     K.[220]. 762
gi 30352025   531 PVSVPSQDMLLGLYALT.[3].R.[127]. 678
gi 139390339  527 PISVPTQDMLIGLYVLT.[3].R.[133]. 680
gi 124112109  519 PIIAPSQDMILGCYYLT.[3].P.[178]. 717
gi 159161244  534 PISVPTQDMLIGLYVLT.[3].H.[137]. 691
gi 11467372   509 PIVTPSQDMVLGCYYLT.[3].L.[107]. 636
gi 150251450  527 PISVPTQDMLLGLYILT.[3].N.[126]. 673
gi 34501435   524 PVSVPSQDMLLGLYILT.[3].H.[127]. 671
gi 134093188  534 PISVPTQDMLMGLYVLT.[3].R.[135]. 689
Citing CDD
Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH. (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 35: D237-40
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